Populations of jellyfish, Mastigias sp., landlocked in tropical marine lakes during the Holocene, show extreme genetic isolation (0.74 < or = phiST < or = 1.00), founder effects (genetic diversity: 0.000 < or = pi < or = 0.001), rapid morphological evolution, and behavioral adaptation. These results demonstrate incipient speciation in what we propose may be modern analogues of Plio-Pleistocene populations isolated in ocean basins by glacially lowered sea level and counterparts to modern marine populations isolated on archipelagos and other distant shores. Geographic isolation in novel environments, even if geologically brief, may contribute much to marine biodiversity because evolutionary rates in marine plankton can rival the most rapid speciation seen for limnetic species, such as cichlids and sticklebacks. Marine lakes present situations rare in their clarity for studying evolution in marine taxa.