The urgent need to integrate evolutionary theory into applied habitat management and land-use planning endeavors has become a focus for much conservation and biodiversity related research. Only recently have scientists begun to incorporate a holistic ecosystem approach, focusing on relationships among plant and animal resources rather than on individual species, into their management philosophies. Swept up in these emerging efforts to sustain biological diversity and functional ecosystems, genetic concepts have been incorporated into habitat management with an alarming mixture of excellence, generalization, and unfortunately even misconception. This does not imply that evolutionary theory has no bearing on the applied sciences but rather that more attention must be given to the interface between theoretical and applied research. The need to integrate genetic theory into ongoing conservation and management efforts is clear; however, much controversy remains as to how this integration may be accomplished for individual management situations. For vertebrates, the transfer of genetic information between generations or within and among various breeding components of populations is inextricably linked to the ecosystem in which they exist. Changes in the structure of an ecosystem can and must influence the ecology of its component species to some extent. However, genetic consequences resulting from changes in the ecology of species or species complexes are not clearly understood. Undoubtedly, alterations in the transfer and conservation of genetic information occur concomitantly with large-scale changes in the landscape. It is likely that these small undetected changes at the genetic level impact species to a similar extent as larger more obvious landscape level factors. In this work we will discuss concepts that are integral to the long-term existence of organisms in managed landscapes and to maintenance of gene diversity in general. Specifically, we will focus on the concept of effective population size, confusion associated with this concept, and its applicability to the maintenance of biologically diverse and sustainable landscapes.