Benthic diatoms are the most common epiphytes on the surfaces of marine organisms. Although some epiphytic diatoms cause multimillion-dollar economic losses in commercially cultivated red algal plantations every year, such as Pyropia (formerly Porphyra), little is known about endophytic or pathogenic diatoms. We found a gomphonemoid diatom species that lives and reproduces inside some marine red algae from two localities on southeast Kamchatka. Both young and old infected host algae were collected in different years (2008 and 2012) and months (July, August, November) from two localities. Numerous brown patches were observed on the surface of red algal thalli. These patches contained a single species of endophytic diatom growing densely in the medullar layer of the host red algae. Some diatom cells were observed in between the filaments composing the cortex. Numerous dividing cells were present in the colonies, indicating that diatoms divided in hospite. In some old host plants, abundant diatom development caused warping of the thalli. Using electron microscopy the endophytic diatom was identified as Pseudogomphonema sp. Phylogenetic analysis based on rbcL gene sequence data revealed that it had 96.6% identity with an isolate from GenBank identified as Pseudogomphonema cf. kamschaticum. This is the first report of Pseudogomphonema living inside macroalgae and being a potentially pathogenic organism.