In this paper we describe a new species, Archaeperidinium saanichi sp. nov. within the Archaeperidinium minutum Jörgensen 1912 species complex. We examined the morphological variation of the cyst and motile stage by incubation experiments from sediment samples collected in coastal British Columbia (Canada), and compared it to closely related species. The theca of A. saanichi is differentiated from related species by overall size, the asymmetry of the intercalary plates and the right-sulcal plate (S.d.) not touching the cingulum. We provide a key to differentiate all closely related species. A. saanichi can be readily distinguished from A. minutum by a distinctively large cyst with a broad 2a type archeopyle and regularly spaced processes with relatively broad bases and aculeate process tips. Molecular phylogenetic analyses of large and small subunit (LSU and SSU) rDNA sequences demonstrated a close affinity of this species to A. minutum; however, the relatively high level of sequence conservation in dinoflagellate rDNA sequences made these particular markers inadequate for distinguishing one species from the other. Sediment-trap data suggest that A. saanichi has a preference for cooler temperatures and lowered salinities.