We propose a biodiversity credit system for trading endangered species habitat designed to minimize and reverse the negative effects of habitat loss and fragmentation, the leading cause of species endangerment in the United States. Given the increasing demand for land, approaches that explicitly balance economic goals against conservation goals are required. The Endangered Species Act balances these conflicts based on the cost to replace habitat. Conservation banking is a means to manage this balance, and we argue for its use to mitigate the effects of habitat fragmentation. Mitigating the effects of land development on biodiversity requires decisions that recognize regional ecological effects resulting from local economic decisions. We propose Landscape Equivalency Analysis (LEA), a landscape-scale approach similar to HEA, as an accounting system to calculate conservation banking credits so that habitat trades do not exacerbate regional ecological effects of local decisions. Credits purchased by public agencies or NGOs for purposes other than mitigating a take create a net investment in natural capital leading to habitat defragmentation. Credits calculated by LEA use metapopulation genetic theory to estimate sustainability criteria against which all trades are judged. The approach is rooted in well-accepted ecological, evolutionary, and economic theory, which helps compensate for the degree of uncertainty regarding the effects of habitat loss and fragmentation on endangered species. LEA requires application of greater scientific rigor than typically applied to endangered species management on private lands but provides an objective, conceptually sound basis for achieving the often conflicting goals of economic efficiency and long-term ecological sustainability.