Preparations for Sunday's season-opening Qatar Grand Prix stepped up a gear on Thursday, and racing under lights at Lopsil, it was Marquez's Repsol Honda that was fastest, the Spaniard posting a time of 1:55m.281s.
The 22-year-old's mark was 0.076s faster than that of his team-mate Dani Pedrosa, while Aleix Espargaro on a Suzuki was next best having posted a time of 1m55.685s.
Yamaha rider Jorge Lorenzo and LCR Honda's Cal Crutchlow were fourth and fifth, having posted times of 1m55.698s and 1m55.818s respectively.
Danilo Petrucci of Pramac Racing and Andrea Dovizioso in the first Ducati were the only other riders to post times below the 1m:56s mark.
Pramac's Yonny Hernandez came home in eighth, just in front of a frustrated Valentino Rossi who had to settle for a time of 1m56.162s. Andrea Iannone's Ducati rounded out the top ten.
Position Rider Team Bike Time Gap Laps
1 Marc Marquez Honda Honda 1m55.281s – 15
2 Dani Pedrosa Honda Honda 1m55.357s 0.076s 15
3 Aleix Espargaro Suzuki Suzuki 1m55.685s 0.404s 13
4 Jorge Lorenzo Yamaha Yamaha 1m55.698s 0.417s 17
5 Cal Crutchlow LCR Honda 1m55.818s 0.537s 16
6 Danilo Petrucci Pramac Racing Ducati 1m55.939s 0.658s 15
7 Andrea Dovizioso Ducati Ducati 1m55.980s 0.699s 17
8 Yonny Hernandez Pramac Racing Ducati 1m56.139s 0.858s 14
9 Valentino Rossi Yamaha Yamaha 1m56.162s 0.881s 18
10 Andrea Iannone Ducati Ducati 1m56.315s 1.034s 17
11 Pol Espargaro Tech 3 Yamaha 1m56.361s 1.080s 18
12 Scott Redding Marc VDS Honda 1m56.374s 1.093s 16
13 Bradley Smith Tech 3 Yamaha 1m56.428s 1.147s 20
14 Stefan Bradl Forward Racing Yamaha Forward/Yamaha 1m56.577s 1.296s 18
15 Karel Abraham AB Motoracing Honda 1m56.651s 1.370s 15
16 Alex de Angelis IodaRacing Project ART/Aprilia 1m56.768s 1.487s 16
17 Maverick Vinales Suzuki Suzuki 1m56.922s 1.641s 14
18 Hector Barbera Avintia Racing Ducati 1m56.957s 1.676s 12
19 Jack Miller LCR Honda 1m56.983s 1.702s 16
20 Loris Baz Forward Racing Yamaha Forward/Yamaha 1m57.031s 1.750s 15
21 Nicky Hayden Aspar Honda 1m57.052s 1.771s 14
22 Alvaro Bautista Aprilia Gresini Aprilia 1m57.130s 1.849s 16
23 Eugene Laverty Aspar Honda 1m57.224s 1.943s 17
24 Mike Di Meglio Avintia Racing Ducati 1m57.612s 2.331s 15
25 Marco Melandri Aprilia Gresini Aprilia 1m59.579s 4.298s 14