When walking in Crete, it is not unusual to come across a dead goat lodged high in the branches of a tree. Like that taverna delicacy from the same animal, boiled entrails, the spectacle takes a little while to digest. Could it be a sacrifice to the old Greek gods? Or carrion left by one of the giant vultures that haunt the island’s craggy slopes?

The truth is no less curious. During the 2m years since Crete reemerged from the Mediterranean, its plants have evolved a unique array of defences against browsing animals. Some bristle with spines or taste so disgusting that a goat will spit them out. Others hug the ground too closely for cropping, or sprout from inaccessible rock faces. So the goats are driven by mounting desperation into the trees for food, some never to descend.

Mercifully, plants odious to goats and sheep are a boon to walkers: nature’s prickly defences sparkle with flowers as vibrant as blooms on a coral reef. Just don’t sit on one. Crete has many more endemic plants than any other European island, and their splashes of colour can hold you spellbound while you inhale the herbal scents of sage, thyme and oregano. Clouds of yellow butterflies and classical olive groves make the senses reel.

Here, along twisting mountain paths, lies the hidden cultural landscape of the Greek island. For there are two Cretes – the Crete of the coast, with its swarming tourists and Minoan palaces; and the Crete of ancient mountain villages, where the lifestyle of shepherds and farmers has outlasted the island’s occupation by Romans, Arabs, Byzantines, Venetians, Turks and Nazis.

You can probably learn as much about Crete by going off the beaten track as you can at archeological sites and museums, which sometimes leave visitors unsatisfied. Besides, walking offers a free show that lifts spirits and burns off the kleftikos.

With 15 mountain ranges and more than 100 gorges, Crete is a walker’s paradise. The most challenging climbs are in the western or central regions, notably the White Mountains and Idean Mountains, both topping 8,000ft. But two considerations influenced my decision to base myself in the eastern port of Agios Nikolaos, once synonymous with the worst excesses of Cretan tourism.

The trouble with the western mountains is that a long journey often precedes walks, most of which are not circular. This means you have to catch a bus to village A and then walk in a state of clenched anxiety to village B in the hope that the afternoon’s only bus has not departed. The experience can leave you shattered.

By contrast, Agios Nikolaos lies only 15 minutes from the mountains. Better still, my landlady turned out to be an Englishwoman who has published a guide of enthralling circular trails that liberate walkers from the bus service and put them back in control behind the wheel of a hire car.

Anne Bouras was a Buckinghamshire girl who came to Crete 30 years ago to work for Hertz. She stayed on to marry Vasilis, a Greek sailor who was setting up a restaurant business, and raise a family. With a friend, Caris Gallos, she began exploring the mountains as recently as 1995. “Our walks always lasted seven or eight hours because we kept getting lost,” she recalled. “I started keeping a diary in case I forgot the way.”

There is something very English about her perseverance in the face of Cretan bemusement. “Greeks don’t go walking unless there is some purpose, such as picking wild greens, which come up after the first rains in September,” she told me. Donkeys have been replaced with 4WD pickup trucks, so some paths have been bulldozed and others fenced off, requiring Anne and a small band of enthusiasts to waymark the new twists with red paint.

Yet a network of trails, some overgrown, still stretches into the hinterland. “I’m still exploring and coming across places I haven’t been to,” said Anne. During the walking seasons (April to June, and September to October) she takes small groups of walkers on her trails.

My first walk from her book soon conjured scenes from Cretan history and the geological forces that have shaped the island. A few miles above Kritsa, a village selling traditional embroidery and tourist knickknacks, a goat path led to a thick black water pipe where bees were drinking from a leak. Dozens of wooden hives, painted in dual colours, were a reminder of the honey that was once exported from Candy, as the island was known to the Venetians. The music of bees and the wind’s sighs turn paths into soundtracks.

Higher up the trail, caterpillars launched themselves from pine trees, abseiling fast down silken ropes like tiny ninja warriors. I read somewhere that beekeepers sometimes introduce caterpillars into pine forests to stimulate the flow of sap, which produces honey tasting of retsina. They can also have the effect of killing the trees, Anne pointed out later.

The track soon became a long, winding staircase of rough stone that must have required a huge investment of labour in ancient times. This was no donkey path, but a road that once linked communities. It dipped steeply into a gorge, another distinctly Cretan phenomenon. Tectonics, rather than flash floods, have carved these deep clefts across the island.

Crete first emerged from the sea 70m years ago, only to sink beneath the waves until the Mediterranean almost dried up about 5m years ago, leaving the island sitting on a mountain range of almost Himalayan proportions. Subsidence and upheaval cracked the rock like masonry, creating gorges as deep as 1,000ft.

I never saw a dead goat in a tree, but a sheep drama awaited towards the end of the walk. Oblivious to my presence, two sparring rams backed off 10yd and accelerated towards each other with an explosive clash of horns. They repeated this brain-crunching performance a dozen times before a ewe diplomatically moved between them and broke up the fight.

Spectacular views, abandoned villages and the kindness of shepherds were features of the next fortnight. Perhaps the most telling insight into the continuum of Cretan life was a visit to the Lasithi Plateau, a cluster of 17 villages, which, at an altitude of almost 3,000ft, ranks as the highest permanently inhabited region of Greece. Its fame brings coachloads of visitors, but tourism still barely impinges on the traditional work of tending vegetable plots, sheep and orchards of apples, pears, plums, cherries and nuts.

Travel brief

Getting there: there are direct flights to Heraklion from 12 UK airports, with airlines including Thomsonfly (0870 190 0737, www.thomsonfly. com), XL Airways (0870 320 7777, www.xl.com) and British Airways (0870 850 9850, www.ba.com).

Where to stay: in Agios Nikolaos, the St Nicolas Bay Hotel (00 30 28410 25041, www.stnicolasbay.gr) is a swish resort-style hotel, with doubles from £176. Or try the Minos Beach Art Hotel (00 30 2 8410 22345, www.bluegr.com), with B&B doubles from £85. Tour operators: for walking holidays in the west of the island, contact Inntravel (01653 617949, www.inntravel.co.uk) or Headwater Holidays (0870 066 2650, www.headwater.com).

Independent walking: look at Circular Walks & Gorges in East Crete by Anne Bouras and Caris Gallos (www.hellenic-books.com £9.95); Landscapes of Eastern Crete by Jonnie Godfrey and Elizabeth Karslake (Sunflower Books £10.99); or Walks in Eastern Crete (Rother Walking Guides £10.99). All are available in Agios Nikolaos. For advice or walking tours, call Anne Bouras on 00 30 28410 25729, or e-mail bousoulas@agn.forthnet.gr.

Times recommends

• The HQ of the great morairaway.com villa scam: a postbox
• The bloggers' travel guide to. . . Copenhagen and Malmö
• A Devon holiday with mates - on a budget