Pliocaenicus seczkinae Stachura-Suchoples, Genkal & Khursevich, sp. nov. was described from the phytoplankton samples and surface bottom deposits of Lake Elgygytgyn located in central Chukotka, NE Russia. The species is distinguished from the nominate variety of P. costatus mainly by the different structure of the valve face fultoportulae, which open externally with distinct short tubes and are flanked by two satellite pores. The tubes are located in small depressions within the radial rows of areolae. These observations have important implications for the entire genus, as up until now all known Pliocaenicus species had external fultoportulae openings lacking tubuli were reported for. Pliocaenicus seczkinae is the second known species of the genus Pliocaenicus to be found in modern populations.