Paes retained his seventh spot in the rankings released today, but Sania slipped to 12th in the doubles list of the WTA charts, thus failing to secure the top-10 ranking that was needed to book a London berth.
Sania would now have to depend on a wildcard to get an entry into the Games.
The top-10 rankings in doubles in both the men and women categories are eligible for direct qualification in the quadrennial event.
Today was the cut-off date set by the International Tennis Federation (ITF) for direct qualification on the basis of the rankings.
Only Paes, among the Indians, was expected to get a direct entry at the Games.
But who between Rohan Bopanna (12th) and Mahesh Bhupathi (14th) would partner Paes or whether India would field two teams during the Olympics, will be decided by the All India Tennis Association (AITA) selection committee, which is scheduled to meet on Friday.
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The ITF, on its part, has set June 21 as the deadline to confirm the entry of eligible players for the Olympics.
AITA will try to get a wildcard for Sania as she has failed to make it to the mega event on merit. Paraguay's Veronica Cepede Royg and Liechenstein's Stephanie Vogt have already been offered two of the four wildcards.
Meanwhile, even as Sania and Bhupathi's victory at the French Open mixed doubles event has made them the favourite pair to be fielded in London, Paes could still be chosen to team up with the Hyderabadi girl.