He claimed his ninth pole of the season for Repsol Honda ahead of Sunday's Czech GP.
The 21-year-old Spaniard, who has won all 10 of the 2014 races, topped the times by 0.129sec in qualifying on Saturday as he bids to continue his record-breaking progress.
PRIME SPOT
Marquez clocked 1min55.585 to take the prime starting spot ahead of Italians Andrea Dovizioso (Ducati) and Andrea Iannone (Ducati) on the front row.
Briton Bradley Smith (Yamaha) was fourth, joined on the second row by Spanish pair Dani Pedrosa (Honda) and Jorge Lorenzo (Yamaha).
2014 Czech Republic MotoGP weekend qualification times
MotoGP
1 Marc Marquez (Spain) Honda - 1min55.585
2 Andrea Dovizioso (Italy) Ducati - 1min55.714
3 Andrea Iannone (Italy) Ducati - 1min55.726
4 Bradley Smith (Britain) Yamaha - 1min55.730
5 Dani Pedrosa (Spain) Honda - 1min55.812
6 Jorge Lorenzo (Spain) Yamaha - 1min55.815
7 Valentino Rossi (Italy) Yamaha - 1min55.821
8 Stefan Bradl (Germany) Honda - 1min55.871
9 Pol Espargaro (Spain) Yamaha - 1min55.899
10 Aleix Espargaro (Spain) Yamaha - 1min56.090
Moto 2
1 Esteve Rabat (Spain) Kalex - 2min01.911
2 Thomas Luethi (Switzerland) Suter - 2min02.143
3 Sandro Cortese (Germany) Kalex - 2min02.307
4 Sam Lowes (Britain) Speed up - 2min02.322
5 Simone Corsi (Italy) Kalex - 2min02.514
6 Mika Kallio (Finland) Kalex - 2min02.517
7 Dominique Aegerter (Switzerland) Suter - 2min02.528
8 Marcel Schroetter (Germany) Tech 3 - 2min02.684
9 Jonas Folger (Germany) Kalex - 2min02.846
10 Franco Morbidelli (Italy) Kalex - 2min02.888
Moto3
1 Alex Marquez (Spain) Honda - 2min07.691
2 Isaac Vinales (Spain) KTM - 2min07.914
3 Niccolo Antonelli (Italy) KTM - 2min08.006
4 Alex Rins (Spain) Honda - 2min08.051
5 Miguel Oliveira (Portugal) Mahindra - 2min08.095
6 Jack Miller (Australia) KTM - 2min08.122
7 Alexis Masbou (France) Honda - 2min08.210
8 Efren Vazquez (Spain) Honda - 2min08.337
9 Enea Bastianini (Italy) KTM - 2min08.396
10 Romano Fenati (Italy) KTM - 2min08.461