Muller's fastest lap was within 0.2s of Honda driver Gabriele Tarquini's 2013 Marrakech pole time, but times are expected to fall further as the track conditions on the Moulay El Hassan street circuit improve through the weekend.
Campos Racing's Hugo Valente was the top non-Citroen runner in fourth. The Frenchman's RML-built Chevrolet Cruze edged out factory Honda driver Tiago Monteiro by 0.033s.
Former grand prix driver Monteiro had been down in ninth spot with two minutes of the half hour session remaining. His late progress up the order came at the expense of Rob Huff, who showed strongly throughout the session for his new employer Lada.
The 2012 WTCC champion held fourth spot behind the dominant Citroens for much of the session before finishing sixth.
ROAL Motorsport's pairing of Tom Coronel and Tom Chilton claimed seventh and ninth, sandwiching local hero Mehdi Bennani.
Proteam racer Bennani took a relatively late delivery of his Civic WTCC, and only completed his maiden run in the car last Wednesday at the Tazio Nuvolari circuit in Northern Italy.
Pos Driver Car Time Gap Laps
1. Yvan Muller Citroen 1m44.513s 10
2. Jose Maria Lopez Citroen 1m44.945s +0.432s 12
3. Sebastien Loeb Citroen 1m45.161s +0.648s 12
4. Hugo Valente Campos Chevrolet 1m46.470s +1.957s 10
5. Tiago Monteiro Honda 1m46.503s +1.990s 12
6. Rob Huff Lada 1m46.798s +2.285s 10
7. Tom Coronel ROAL Chevrolet 1m46.927s +2.414s 13
8. Mehdi Bennani Proteam Honda 1m47.583s +3.070s 12
9. Tom Chilton ROAL Chevrolet 1m47.617s +3.104s 11
10. Gabriele Tarquini Honda 1m47.629s +3.116s 13
11. Gianni Morbidelli Munnich Chevrolet 1m47.785s +3.272s 12
12. Dusan Borkovic Campos Chevrolet 1m47.906s +3.393s 10
13. Norbert Michelisz Zengo Honda 1m47.997s +3.484s 11
14. James Thompson Lada 1m48.720s +4.207s 6
15. Rene Munnich Munnich Chevrolet 1m49.135s +4.622s 12
16. Franz Engstler Engstler BMW 1m50.549s +6.036s 12 *
17. Mikhail Kozlovskiy Lada 1m51.767s +7.254s 8
18. Peter Fulin Campos SEAT 1m52.196s +7.683s 14 *
19. Pasquale di Sabatino Engstler BMW 1m52.964s +8.451s 5 *
20. John Filippi Campos SEAT 1m59.529s +15.016s 9 *
Follow the first races of the WTCC's new era as they happen with AUTOSPORT Race Centre Live's coverage from Marrakech, beginning 4pm UK time on Sunday April 13 - and watch video highlights on the AUTOSPORT WTCC page
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