The pelagophyte Aureococcus anophagefferens causes harmful brown tide blooms in marine embayments. Many studies have shown A. anophagefferens can grow in the wide range of environmental conditions seen during blooms. The reference genome, A. anophagefferens CCMP1984, provided genomic evidence for these studies, as well as provided further insights into how A. anophagefferens outcompetes other photosynthetic organisms in the water column. To expand on the genomic tools that exists for this species, genomes for four strains were assembled: three from new sequencing data and one from publicly available data. The coding potentials of all the strains were similar to one another, although each strain possessed unique coding sequences with unique functions. Like the reference genome, the genomes assembled in this study possessed genes hypothesized to be important in bloom proliferation, including genes involved in organic nutrient metabolism and growth at low light, but did not possess the large number of selenocysteine containing proteins. Using pre-existing transcriptomics of a natural bloom it was found that use of a single genome did not result in as much read mapping as compared to a database generated from all genomes, suggesting novel information about bloom ecology can be gained from expanding genomic space. These observations also suggest that the utilization of purines is potentially an important source of organic nitrogen.