Seven new isolates of the heterokont algal class Synchromophyceae are described from coastal habitats of the Atlantic Ocean, including the Caribbean and Mediterranean Seas. All of the new isolates contain chloroplast complexes, a key feature of this group of algae. Morphology, pigments and DNA sequences support a monophyletic grouping of the Synchromophyceae to the exclusion of other Ochrophyta (primarily photosynthetic stramenopiles). Within the Synchromophyceae, two phylogenetic clades based on rbcL and 18S rDNA data were discovered, which differ in cell size and also the number of plastid complexes per cell. Two isolates form a clade with the type species Synchroma grande, while all other isolates form a separate clade, including the newly described species S. pusillum. Further species delineation of the isolates is difficult due to the highly similar morphology and life cycle strategy. Phylogenetic relationships with other genera of the Ochrophyta, such as Leukarachnion and Chlamydomyxa, are apparent and shed light on a heterogeneous branch of heterokont evolution.