Marine phytoplankton perform approximately half of global CO2 uptake. The phytoplankton communities that perform this photosynthesis are diverse and belong to different size classes. In many marine settings picophytoplankton (size) are abundant and among eukaryotic picoplankton the prasinophyte class Mamiellophyceae is particularly well-represented. Three Mamiellophyceae genera found in many marine settings are Micromonas, Ostreococcus and Bathycoccus. This thesis provides analyses of features shared by the Mamiellophyceae, features unique to an individual genus, and overall environmental distributions of the above genera. Specifically, Mamiellophyceae genome features were characterized quantitatively in Micromonas (Chapter 2, 3) and led to the detection of repetitive elements that can be used as tools for identifying Micromonas clades (Chapter 3). Application of these 'markers' to metagenomic data led to the discovery of Micromonas in the Southern Ocean and at salinities and depths it was previously not known to inhabit. In Ostreococcus and Bathycoccus different types of molecular markers were used to define distances between putative ecotypes within these genera (Chapter 4). This analysis showed two coastal Bathycoccus targeted metagenomes belong to the same clade as a cultured species, Bathycoccus prasinos, while sequences from a Tropical Atlantic Bathycoccus belong to a separate clade. Using this comprehension of Bathycoccus and Ostreococcus diversity, ecomarker genes were selected and used to analyze ecotypes of these genera in metatranscriptome and metagenome data. These analyses were combined with qPCR, flow cytometry and nutrient measurements (Chapter 4). The results provided in this thesis improve our knowledge of the diversity and biogeography of members of the Mamiellophyceae class. Collectively, these studies provide a baseline for future comparisons, as speciation and environmental adaptations are ongoing and may increase with global climate change.