Popular Inc. (BPOP) faces an uncertain future even as it puts some of its past behind it by exiting the Troubled Asset Relief Program.

The San Juan, Puerto Rico, company has received regulatory approval to repay $935 million in Tarp funds. It's an important accomplishment for the $36.2 billion-asset company, which has owed the most Tarp money since Synovus Financial (SNV) exited the program last summer. Once Popular exits Tarp, First BanCorp (FBP) in Puerto Rico, which owes nearly $240 million, will become the biggest bank left in the program.

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