A marine ‘chrysophyte’ species Polypodochrysis teissieri Magne having distinctive lorica was re-examined using both light and electron microscopy. Light microscopic observations were basically identical to Magne's descriptions (Magne 1975), except that the aplanospore in that paper was shown to be a distinctive uniflagellate zoospore. General ultrastructure of both chloroplast and mitochondria was typical of the photosynthetic stramenopiles (chromophytes). An embedded pyrenoid was found in the center of chloroplast and was penetrated by the chloroplast envelope. Two Golgi bodies were always located adjacent to the nucleus; they were arranged perpendicularly in vegetative cells, but had a parallel arrangement in zoospores. Thin sections of the lorica resembled siliceous structures such as diatom frustules, but energy dispersive X-ray analysis did not show any significant amount of silicon. Naked zoospores have a single emergent flagellum that lacked mastigonemes; a flagellar swelling and an eyespot were also absent. Zoospores showed gliding motion on the surface of substrate. Two different cytoplasmic extensions (pseudopods) were observed in the zoospore. One lingulate pseudopod originated from the base of the flagellum and was always associated with the flagellum, and the second pseudopod formed only when the cell changed direction. Investigations of the flagellar apparatus showed a single transitional plate in the transitional region of the emergent flagellum, a second basal body closely located to the flagellum-bearing basal body, three microtubular roots and a set of cytoskeletal microtubules, and a small rhizoplast that connected the non-flagellum-bearing basal body and the nucleus. Many features of the zoospore of Polypodochrysis show a similarity with that of Glossomastix chrysoplasta (Pinguiophyceae), suggesting that the single emergent flagellum of Polypodochrysis and Glossomastix is homologous. This single flagellum may correspond to the mature flagellum that is generally recognized as the short posterior flagellum in stramenopiles, and it represents a unique flagellar arrangement within stramenopiles. Based on the morphological features, in addition to the other data (18S rRNA and rbcL genes and biochemical features) published elsewhere, Polypodochrysis was removed from the class Chrysophyceae and transferred to a new class, the Pinguiophyceae.