Honda rider Marquez, who has won all three of this year's races and is competing in his 100th grand prix, clocked 1 minute 38.120 seconds to smash the pole record at the Andalusian circuit, 0.421 seconds ahead of Yamaha's Jorge Lorenzo.
Marquez's Honda team mate Dani Pedrosa was 0.510 seconds off the pace in third to complete an all-Spanish front row.
Decorated Italian rider Valentino Rossi of Yamaha, who has six premier class victories at Jerez, was fourth quickest.
Marquez has won all three of this year's races from pole and tops the championship standings on 75 points. Pedrosa is second on 56 points and Rossi third on 41.
(Reporting by Iain Rogers, editing by Justin Palmer)
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