Flexibility in Rebuilding American Fisheries Act of 2009 - Amends the Magnuson-Stevens Fishery Conservation and Management Act to require fishery management plans, amendments, or regulations for overfished fisheries to specify a time period for ending overfishing and rebuilding the fishery that is as short as practicable (currently, as short as possible). Modifies the exceptions to the requirement that such period not exceed ten years.
Requires consideration, in evaluating progress to end overfishing and rebuild overfished stocks, of factors other than commercial and recreational fishing.
Requires, when the Secretary of Commerce extends the period under specified provisions, that the maximum rebuilding time not exceed the sum of the initial ten-year period, the expected time to rebuild the stock absent any fishing mortality and under prevailing environmental conditions, and the mean generation time of the stock.