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Codex map (made late sixteenth century). Paper; from Mexico

It looks today like the most brutal and the most complete replacement of one culture by another that you could possibly imagine. As you stand in the Zócalo, the main square of Mexico City, listening to the music and bustle, the palace of the Spanish viceroy stands on the very site of the demolished palace of Moctezuma. Along the street you can see the ruins of what was once the Aztec temple, and the sacred Aztec precinct is now largely taken up by the huge Spanish Baroque cathedral dedicated to the Virgin Mary. From here, it looks as if the Spanish Conquest of Mexico in 1521 was in every way cataclysmic for indigenous traditions, and that is how the story has often been told.

The reality, however, was more gradual, and perhaps more interesting. The local people kept their own languages. They also kept their own land, for the most part, although the hideous consequences of the disease that the Spanish had brought with them unwittingly meant that much land was freed up for the new settlers from Spain.

Apart from disease, the most significant new aspect of Mexican life under the Spanish was their religion. Catholic missionaries came with the conquerors in the 1520s, and they transformed the spiritual landscape. Now, five hundred years later, over 80 per cent of the population of Mexico is Catholic. In the process, the physical landscape changed, too. The invaders crushed temples and raised churches all over the Aztec Empire. And the object that we're looking at now shows us exactly how that process was carried out.

"Any visitor to Mexico will immediately realise that you can't really get away from Catholicism - it's everywhere, it's pretty overwhelming." (Fernando Cervantes)

"Many of these Mexican churches are built right on platforms of old pagan temples. These churches, many of them, could be compared to some of the great medieval cathedrals in Europe, certainly in size and grandeur." (Samuel Edgerton)

So far this week, our objects have come from cultures where different faiths have managed to find a reasonably positive way of living together. In India, Iran and Indonesia in the sixteenth and seventeenth centuries, religious tolerance was a hallmark of effective statecraft. But in Mexico one religion came as the instrument of conquest, and was only slowly absorbed by the indigenous population. We can see something of the Spanish imperial methods - and the resilience of local traditions - in this programme's object. It's an annotated map.

It's about two and a half feet (75 cm) wide and one and a half feet (45 cm) high, and it's painted on very rough paper. In fact, when you look closely, you can see that it is bark, that's been beaten in to a sheet of paper. On the map there are squares and rectangles showing, presumably, divisions of fields, with names written onto them to show the owners. There's a small blue river with wavy lines on it, and a forking road with feet on it, showing this is a thoroughfare. And on top of this diagram there are painted images. In the middle there's a tree, with under it three figures wearing European dress. And then the principle features of the map - two large churches. They've both got bell towers, and they're painted in bright colours of pink and yellow. One is labelled Santa Barbara, the other Santa Ana. So this map shows us the indigenous Mexican population and their land-holdings, and the new Spanish churches of the 'conquistadores'.

The map shows us an area in the province of Tlaxcala to the east of Mexico City - a region whose people had bitterly resented Aztec rule, and who had enthusiastically joined the Spaniards in defeating them. This may explain why so many of the names of land-holders on the map show marriages between Spanish settlers and native Indian aristocrats - evidence of a remarkable fusion between the two peoples and the emergence of a new, mixed ruling class. More surprisingly, a similar fusion took place in the church. For example, many communities in the Tlaxcala area had been protected by the native Indian deity Toci, who was the grandmother of the Mexican gods. After the Conquest she was replaced as local patroness by St Anne, who in Catholic tradition was the grandmother of Christ. The grandmother may have changed her name, but it's hard to believe that for the local worshippers she had in any serious way changed her nature.

While in many places the Spanish Conquest was brutal, the conversion of local people to Catholicism was not usually forced. The missionaries were genuinely intent on instilling the true faith, and so regarded compulsory conversion as worthless. But even if many Indians willingly converted, they could surely not have welcomed the destruction of their previous places of worship. Yet this was a key part of Spanish policy. A Franciscan letter written ten years after the Conquest boasts of the achievements of this new, Mexican, church triumphant:

"More than 250,000 men have been baptised, 500 temples have been destroyed, and more than 26,000 figures of demons, which the Indians worshipped, have been demolished and burned."

The two new churches of Santa Barbara and Santa Ana dominate the landscape on our map, and one of them has clearly been built on top of a destroyed native temple. Here's the historian Samuel Edgerton:

"It's a very clever ruse that they did in order to help the Indians feel comfortable now, in the new churches which were literally on top of the old church or the old temples. Anyway, the central church has in front of it a large courtyard. It's what is today called an 'atrio' or a 'patio'. And this was a kind of innovation that the friars introduced to the buildings of these churches in Mexico, because in the beginning the churches were often small, and you could not crowd all the Indians who were being brought in here to be converted. And so you had them stand in this large courtyard, and there they were preached to from an open chapel . . . easier for the church then to work as a 'theatre for conversion' - a word that I sort of invented."

The churches on our map, these theatres of conversion, were built within an existing landscape of roads, water-courses, fields and houses. Interestingly, names and places are given in a mixture of Spanish and the local Nahuatl language. For example, the church of Santa Barbara is shown in a village called Santa Barbara Tamasolco. Tamasolco means 'place of the toad', which almost certainly had a pre-Christian religious significance, now lost. But it's very present on the map, because the artist has drawn a toad just below the place-name. So the two religious traditions live on, combined in the eccentric place-name, Santa Barbara at the Place of the Toad.

They also clearly lived on in the minds of the converted. An inscription on the map tells us: "Juan Bernabe said to his wife, 'Sister of mine, let us give soul to our offspring, let us plant the willows that shall be our memory'. In this lyrical glimpse of private faith, Juan Bernabe, despite bearing two Christian saints' names, obviously still believes that his children's salvation will be achieved in communion with the natural world of native tradition, rather than inside the Catholic church down the road.

The babies of this "new Spain", as the invaders called it, were, like Juan Bernabe, given new Christian names at baptism. But again like Juan Bernabe, it didn't necessarily make them good Catholics. Later reformers would crack down on continuing pre-Christian practices and old rituals. Incantations, divination, mask-wearing - all were punished as sorcery or idolatry. But many ceremonies survived through sheer tenacity on the part of the indigenous people. And the most striking modern example is perhaps the way pre-Christian ancestor veneration has merged with the Christian All Souls Day to create the Day of the Dead. [This is] an entirely Mexican celebration, still vigorously alive, in which every 2nd of November the living remember their dead, with skulls and skeletons in colourful costumes, festive music, special offerings and food. A celebration that owes as much or more to native Indian religious practices than to Catholic piety.

The Nahuatl language that appears on our map has just about survived. A census carried out in 2000 revealed that only one and a half per cent of the population could now still speak it. Recently, however, the Mayor of Mexico City has said he wants all city employees to learn Nahuatl, in an effort to revive the ancient tongue. Quite a few Nahuatl words do in fact survive today - although I don't suppose many of us realise we are using Nahuatl when we talk about tomato, chocolate or avocado. Significantly, but not surprisingly, no religious Nahuatl words have stayed with us. The missionaries' teaching saw to that.

Today, five centuries on, the Mexican people are eager to revive their pre-Hispanic past, as a defining element of their national identity. But in the realm of faith, the Conquest's legacy of Christian conversion is still overwhelming. In spite of its great communist and anti-clerical revolutions of the twentieth century, Mexican identity remains essentially Catholic. As the Mexican-born historian Dr Fernando Cervantes underlines:

"There is a very strong anti-clerical, anti-religious nationalist ideology in Mexico, but it's a very ambivalent type of thing, because even the most atheistic Mexicans will never deny that they are devoted to the Virgin of Guadalupe for instance. This is something that very often comes up, and this is where the Catholic sub-stratum comes through very strongly, that you can't really square the circle of being Mexican and not being in some senses Catholic. I think that this is where you can see how strong the early evangelisation was, and how alive it still is nowadays."

Everything that Dr Cervantes was talking about, indeed everything that our little map reveals about the Christianisation of Mexico, is summed up on a colossal scale here at the shrine of Guadalupe in the suburbs of Mexico City. After the Vatican, this is now the most visited Catholic shrine in the world. It was here, where there had once been an Aztec shrine, that in December 1531, just ten years after the Conquest, the Virgin Mary appeared to a young Aztec man whom the Spaniards called Juan Diego. She asked him to trust in her, and she miraculously imprinted her image on his cloak. A church was built on the site of Juan Diego's vision, the image on the cloak produced miracles and conversions in huge numbers, and the crowds flooded in to Guadalupe. For a long time the Catholic clergy were worried that this was in fact merely the worship of an Aztec goddess, being continued on the site of an Aztec shrine, but the combined forces of the two religious traditions have over the centuries proved irresistible. There are now, in fact, so many visitors to Guadalupe that you have to move in front of the miraculous image on a conveyer belt - as I am doing just now! In 1737 the Virgin of Guadalupe was proclaimed patroness of Mexico, and in 2002 Pope Jean-Paul II declared Juan Diego, the young Aztec born under Moctezuma, a saint of the universal Catholic Church.

In the next programme, we are in Europe, where Catholicism was not trying to oust a long-established, existing faith, but to confront and eradicate a new one. We're in Germany in 1617, a century after Luther, and in the middle of the counter-Reformation . . . with a woodblock print, and some very vigorous Protestant propaganda.