Conservation efforts should strive to ensure that genetic diversity is preserved, so that evolutionary potential is maintained within a species. This is a two-part problem: 1) to accurately assess biological diversity, and 2) to estimate the current or historical dynamic among populations within lineages.  A combination of molecular phylogenetic techniques and population genetic methods can be used to identify evolutionary lineages and reconstruct their genealogical relationships.  Such information reveals natural groups that can then be managed as separate conservation units to preserve their genetic integrity and evolutionary potential. I will discuss recent progress and major challenges in the conservation of benthic organisms and how molecular techniques can be widely applied.  In particular, I will focus on techniques developed for fisheries science, which provide tools and guidelines that will be critical to successful management efforts.  Finally, I will recommend molecular guidelines for the conservation of benthic organisms, using unionid mussels as an example.