A new diatom species, Halamphora primus sp. nov. is here proposed, and described based on comparison of morphological traits. This new taxon has semi-lanceolate valves, strongly dorsiventral. Its ventral margin goes from slightly concave in the mid part to lightly convex toward the eccentric parts. Unlike most species of Amphora sensu lato that have the raphe distal ends curved dorsally, in H. primus these are curved ventrally. A ledge is present on the dorsal side of raphe, and a short conopeum extends along the raphe sternum fading before reaching the apices. A dorsal fascia is absent. Specimens were collected along with a highly diverse taxocoenosis (S=281) from the skin of stonefish in the Gulf of California, Mexico. However, the scarceness of H. primus frustules in the sampled taxocoenosis strongly suggests that it is not an epizoic form of the stonefish.