The short answer
Both routes are worth doing. Most travelers find Marrakech → Fes (via Merzouga or the standard desert route) flows naturally if starting in Marrakech. Fes → Marrakech is equally sensible if you're finishing in Marrakech for flights.

The classic desert transfer between Morocco's two imperial cities can go either way. Direction affects scenery, timing, and how you experience the journey through the Atlas and Sahara.
Both routes are worth doing. Most travelers find Marrakech → Fes (via Merzouga or the standard desert route) flows naturally if starting in Marrakech. Fes → Marrakech is equally sensible if you're finishing in Marrakech for flights.
The desert route between them typically passes through the High Atlas mountains, Ouarzazate, Dades Valley, Todra Gorge, and either Erg Chebbi (Merzouga) or Erg Chigaga. It's usually done as a 3-day or 4-day tour with an overnight in the desert.
The distance is similar either way - around 530-560 km depending on exact route and stops.
Whichever direction you choose, you'll cross the High Atlas via Tizi n'Tichka pass, stop at Ait Ben Haddou (UNESCO), explore the dramatic gorges, and spend a night in a desert camp with camel trekking and stargazing.
The desert experience (dunes, camp, sunrise) is the highlight regardless of direction.
Don't stress too much about direction. The route works either way. Choose based on your flight itinerary and where you want to spend your final days in Morocco. Both are equally rewarding when done as a private or small group tour with experienced guides. You can see both directions in practice on the three-day Marrakech to Fes desert tour and the four-day Fes to Marrakech desert tour.

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