Playing in his first tournament since winning his record-setting 11-hour match against Nicolas Mahut during the first round at Wimbledon, Isner defeated Muller 4-6, 7-6 (8-6), 7-6 (9-7). The match lasted 2 1/2 hours.
The 33 aces ran Isner's total for the season to an ATP Tour-leading 705. Isner will next meet Michael Russell, who advanced with a 1-6, 6-2, 7-5 win over Rainer Schuettler.
Mardy Fish, the sixth seed, moved into the third round by downing Robby Ginepri 6-1, 7-5. Taylor Dent, who defeated Horacio Zeballos 4-6, 6-2, 6-0, will face Fish in the next round.
Top-seeded Andy Roddick will play his second-round match Thursday against Rajeev Ram.
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