Kryptoperidinium belongs to a group of dinophytes hosting a diatom as an endosymbiont and is currently considered to comprise a single, putatively bloom-forming and harmful species only. Molecular phylogenetics indicate the existence of a second distinct lineage and therefore species new to science, which we here formally describe as Kryptoperidinium secundum sp. nov. We studied living and fixed material of unialgal strains in detail using light and electron microscopy and gained DNA sequences of the rRNA complex (hosts and endosymbionts, from which also psbA and rbcL sequence data were obtained). In a molecular phylogeny of the Bacillariophyceae, the endosymbionts of K. secundum have a divergent position from those of Kryptoperidinium triquetrum (=K. foliaceum) and show (once more) a close relationship to free-living diatoms. The cells of K. secundum were strongly dorso-ventrally compressed and exhibited the thecal plate formula po, X, 4', 2a, 7'', 5C, 6(?)S, 5''', 2''''. The distalmost precingular plate was consistently rectangular in shape and relatively broad, and this is the key diagnostic trait to distinguish K. secundum from the known K. triquetrum, which has a characteristically L-shaped plate with a thin and elongated base. The two species are clearly divergent in molecular phylogenetics (exhibiting long branches) and constitute a monophyletic group together with Dinothrix sharing the same thecal plate formula. The diatom phylogeny favours an evolutionary scenario of repeated plastid capture rather than strict co-divergence between dinophyte hosts and their endosymbionts.