We report on taxonomically distinguishing morphological features of six diatom taxa from the marine, nanoplanktonic genus, Minidiscus, found in Eastern Canada and neighbouring waters. Four of the six were also investigated using genetic approaches. We found that the culture deposited in the Provasoli-Guillard National Center for Culture of Marine Phytoplankton (CCMP) as CCMP 496 was morphologically closest to the published type image of M. trioculatus, whereas other isolates were morphologically and/or genetically divergent. Consequently, we propose three new taxa. One monoclonal line isolated from the Bay of Fundy is proposed as a new variety, M. trioculatus var. monoculatus. The well-studied nanoplanktonic diatom strain, CCMP 495, currently considered to be 'M. trioculatus' was morphologically and genetically divergent from CCMP 496 and we propose specific status for it, M. variabilis. We isolated a new strain from the Gulf of St Lawrence that was nearly genetically identical in 18S and ITS regions to CCMP 495, but showed distinct morphological differences and we propose a new form for this strain. Culture-based data were supplemented by those from natural seawater whenever possible. Two species (M. comicus, M. chilensis) known from our region, but unavailable in culture, are presented for comparison.