Transparent and Science-Based Fishery Management Act of 2012

Transparent and Science-Based Fishery Management Act of 2012 - Amends the Magnuson-Stevens Fishery Conservation and Management Act to provide that a Regional Fishery Management Council is not required to develop an annual catch limit for: (1) an ecosystem component species; or (2) a species, fishery, or stock for which a survey and stock assessment have not been performed within the preceding five years.

Defines "ecosystem component species" as a stock of fish that is a nontarget, incidentally harvested stock of fish in a fishery, or a nontarget, incidentally harvested stock of fish, that a Council or the Secretary of Commerce has determined is not: (1) subject to overfishing, approaching an overfished condition, or overfished; and (2) likely to become subject to overfishing or overfished in the absence of conservation and management measures.

Requires each annual catch limit to take into account: (1) management measures under international agreements in which the United States participates, and (2) informal transboundary agreements under which management activities outside the exclusive economic zone by another country may hinder conservation efforts by U.S. fishermen for a species for which any of the recruitment, distribution, life history, or fishing activities are transboundary.

Prohibits the New England, Mid-Atlantic, South Atlantic, and Gulf of Mexico Councils, except with respect to the Gulf of Mexico commercial red snapper fishery, from submitting a fishery management plan or amendment that creates a catch share program for a fishery (and prohibits the Secretary from implementing a secretarial plan or amendment) unless the final program has been approved in a referendum by a majority of specified permit holders eligible to participate in the fishery.

Requires 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 (under current law, as short as possible). Modifies exceptions to the requirement that such period not exceed 10 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 extends the rebuilding period under specified provisions, that the maximum rebuilding time not exceed the sum of the initial 10-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.

Permits the Secretary to: (1) suspend annual catch limits under specified circumstances, and (2) use portions of fisheries enforcement penalties for data collection purposes.

Directs the Secretary to review and report to Congress on each fishery closure under federal law for which notice was published in the Federal Register that was not a normal and expected occurrence under the fishery management plan for the fishery concerned and was considered disruptive to sport, charter, or commercial fishing operations, and that was in effect for more than 120 days within the five-year period preceding the enactment of this Act.