Isner dropped Sunday's final to Juan Monaco 6-2, 3-6, 6-3 but continued to play solidly on clay -- not generally the surface of choice for American men tennis players.
Isner won a pair of matches on clay a week ago in helping the United States advance in Davis Cup play against France and won his first three matches in Houston to reach Sunday's finals.
The 150 rankings points he earned at the Clay Court Championship moves him past countryman Mardy Fish and into ninth in the ranking by 45 points.
Novak Djokovic is No. 1, a position he's held for 43 weeks. That's tied with Gustavo Kuerten for 12th most.
Djokovic has 12,670 points, which will increased this week because he's entered into the Monte Carlo Rolex Masters, an event he missed in 2011. Seven-time defending Monte Carlo champion Rafael Nadal is second with 9,215 points while Roger Federer (8,880) sits in third and Andy Murray (7,680) remains No. 4.
Jo-Wilfried Tsonga is in the fifth spot with 4,795 points while David Ferrer (4,280) is No. 6 with Tomas Berdych in seventh with 3,810.
Janko Tipsarevic (2,820) is eighth but is only 50 points ahead of Isner and Fish has 2,725 points.
Monaco matches his career best by moving to No. 14 in the rankings. Pablo Andujar, who repeated Sunday as champion of the Grand Prix Hassan II in Morocco, jumps 19 spots to No. 39 in this week's rankings.
Seven of the Top 10 players are in the field for this week's Monte Carlo Masters. Federer, Isner and Fish are skipping the event.
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