Four days in Bukhara: the old town Samarkand does not have

Arrive, drop the bag, and start where the town gathers. The Lyab-i Hauz pool was dug in 1620, the last survivor of dozens that once watered Bukhara and gave it a fearsome reputation for waterborne disease, which the Soviets solved by filling almost all of them in. Mulberry trees as old as the pool lean over the water, old men play chess under them, and on two sides stand madrasas: Nadir Divan-Begi, with a pair of mythical birds and a human-faced sun on its portal in flagrant defiance of the rules about depicting living things, and Kukeldash, one of the largest Quranic schools ever built in Central Asia.

Behind the pool, in the lanes to the south, is the synagogue. Bukharan Jews have been here since at least the eighth century and had their own dialect of Persian, their own liturgy and, until the 1990s emigration, a community of thousands. The building dates from around 1640 and, by local legend, was part of the settlement with the widow whose land was seized to dig the pool. It is small, still in use, and someone will show you round.

Walk east afterwards to Chor Minor, which means four minarets and is not a mosque gate to anything any more, because the madrasa it belonged to has vanished. Built in 1807, it is a squat brick box with four towers capped in blue tile, each one decorated differently, standing on its own in a residential lane. One tower fell down in 1995 and was rebuilt. It is the least grand thing in Bukhara and the one that ends up on people's walls.

Today is one straight walk west, and it takes all day because you keep stopping. Start at Magok-i-Attari, a few minutes from the pool, sunk four or five metres below the modern street because the town has spent a thousand years rising on its own rubble. It is the oldest mosque building left in Central Asia, with a deeply carved brick and terracotta facade of the twelfth century, standing over the remains of a Zoroastrian temple. It is a carpet museum now, which is a fair use for it.

Then the domes. Three of the covered crossroads that housed the specialist bazaars survive, rebuilt in the sixteenth century over much older markets, and each one had a trade: money changers, cap makers, jewellers. Toqi Telpak Furushon is the hat sellers' one, and there are still hats, along with knives, miniatures and a great deal of carpet. Walk through slowly. The domes themselves, with their honeycombed corner vaults and their shafts of daylight, are better than most of what is being sold under them.

The walk ends at Po-i-Kalyan, which is the set piece. The minaret was finished in 1127, stands about 46 metres, and is built of plain baked brick in fourteen bands of different geometric pattern with no colour on it until the gallery at the top. Genghis Khan reportedly spared it when he destroyed everything around it. Criminals were thrown from the top into the square below, which is why nineteenth century travellers called it the Tower of Death. On one side is the Friday mosque, rebuilt in the early sixteenth century around a courtyard that holds twelve thousand; on the other the Mir-i-Arab madrasa, which is still a working seminary and was one of the very few allowed to keep teaching through the Soviet period.

The Ark is the mound at the west end of the old town, an artificial hill with a mud-brick citadel on top that was the seat of the emirs and, before them, of every ruler here since about the fifth century. It is entered up a ramp between two towers, and inside are the throne court, the mint, the mosque and the stables, plus a lot of open ground: the Red Army shelled and bombed the place in 1920 and roughly four fifths of the interior never came back. The story people come for happened just outside, where two British officers, Stoddart and Conolly, were held in a pit full of vermin and beheaded in 1842 during the diplomatic manoeuvring between Russia and British India.

Facing the Ark across the square is Bolo Hauz, and it is the prettiest building in Bukhara. The mosque was built in 1712 as the emir's own Friday mosque, and the porch that makes it was added in 1917: twenty tall wooden columns, painted and carved, with a pool in front of them, so that in still water there appear to be forty. It is still in use, so take your shoes off and keep quiet.

Then into the park behind for the Ismail Samani mausoleum, which does not announce itself at all. It is a brick cube about ten metres a side with a dome on top, built around the turn of the tenth century for the founder of the Samanid dynasty, and every surface inside and out is basketwork brickwork laid so that the pattern changes completely as the sun moves. There is no tile, no paint and no inscription of any size. It is the oldest Islamic building standing in Central Asia and the best, and it survived the Mongols because by then it was buried in silt and nobody knew it was there.

Hire a car for the morning, because both of today's places are outside town and neither takes long. Start north at Sitori-i-Mokhi Khosa, the summer palace of Alim Khan, the last emir of Bukhara. It was finished in 1918. He was overthrown in 1920 and fled to Afghanistan, so he barely used it. The design is a straight collision of two tastes, with Russian-trained architects doing the outside and Bukharan craftsmen the inside: parquet, chandeliers and a white hall of mirrored ganch plasterwork that took several years, alongside courtyards, peacocks and a pool where, according to a story every guide tells, the emir watched his harem swim from a balcony. Take that one with salt. The costume and suzani collection upstairs is genuinely good.

Then east to Baha al-Din Naqshband, ten kilometres out, which is the most important Sufi shrine in Uzbekistan and a completely different kind of visit. Naqshband died in 1389 and gave his name to the Naqshbandi order, which spread from here across the Islamic world as far as Indonesia and Bosnia. The complex around his tomb is a large open courtyard of mosque, minaret and pool, and it is full of Uzbek pilgrims rather than visitors: families circling the grave, a wishing tree, and a mulberry stump that people touch for luck. Dress properly and stand still for a while.

Back in time for an afternoon train. Remember that Kogon station is 15 km out, so leave an hour for a journey that looks like twenty minutes.