Goniomonads are commonly found heterotrophic biflagellates in both marine and freshwater environments. Despite the high genetic diversity inferred from 18S rDNA data, many goniomonad species remain undescribed. In this study, we established a total of 21 marine goniomonad culture strains, and from these, describe three new species by using 18S rDNA phylogeny, light microscopy, and electron microscopy. Molecular sequence analyses suggest the presence of several distinct sub-lineages within the marine goniomonad clade. Two of these are Goniomonas ulleungensis sp. nov. and G. lingua sp. nov., which are similar in size, flagellar length, appendage, and orientation and have a tongue-like protrusion at the anterior. The two species can be differentiated by the periplast plate pattern with G. ulleungensis displaying one additional plate on the right side. G. duplex sp. nov. differed from these two species by having two unequal flagella with the longer one trailing posteriorly and having the opposite cell orientation when skidding. Comparative analyses of five marine goniomonad species showed that genetically distinct goniomonad groups can be delineated by morphological data as well, and of several morphological features that are of taxonomic utility, the periplast plate pattern, observable by SEM, is particularly informative in goniomonad taxonomy.