Previously assigned to the genus Pichia based on phenotypic traits, Scheffersomyces spartinae is a marine yeast that is commonly isolated from brackish water environments and associated oyster grass. Assignment to its current genus remains controversial due to poor bootstrap support, phenotypic traits, and a lack of genomic sequence data. Scheffersomyces spartinae strain ARV_011 was isolated from the Great Sippewissett Marsh in Falmouth, Massachusetts. Strain ARV_011 exhibits a high population of cells with enlarged vacuoles containing unknown fast-moving granules. To further investigate the observed granules as well as the taxonomic placement of the species, we sequenced the Scheffersomyces spartinae strain ARV_011 genome.