We describe the biogeography of two clades of Bathycoccus, a picoplanktonic group of marine green algae, that are phylogenetically distinct based on analysis of the ITS1/5.8S/ITS2 region of the nuclear rRNA operon, but identical across the 18S rRNA gene. QPCR assays were developed against the ITS1 to allow quantification of these taxa (clades BI and BII). These were used alongside prior 18S rRNA primer-probes for two Ostreococcus clades that have previously been classified as different ecotypes (clades OI and OII) to analyze 266 photic zone samples from the tropical Atlantic and North Pacific Oceans. Clades BI and OI were observed in mesotrophic locations, whereas BII and OII were found in oligotrophic regions. Bathycoccus ecotypes co-occurred more often than Ostreococcus ecotypes. In contrast to Ostreococcus ecotypes, the adaptive differences between Bathycoccus clades have yet to be resolved and both Bathycoccus ecotypes appear to be more flexible in their niche(s) than Ostreococcus.