An important aspect of marine biodiversity studies is identification of species and subspecies complexes. Here we present a number of examples from marine algae in which allozymes, DNA sequences and RAPDs are used to identify cryptic species and explore phylogenetic-population level relationships over several biogeographic spatial and temporal scales. In addition to evidence for recent dispersal over large distances, effects of present and past climates are reflected in the phylogenetic history of many biogeographic complexes. In some cases temperature adaptations can also be detected. Phylogeographic studies on coastal seaweeds and oceanic phytoplankton which utilize molecular genetic data contain a wealth of previously unrecognized information relevant to biodiversity.