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A new species of Protaphorura Absolon, 1901 (Collembola, Onychiuridae), P. cykini sp.nov., is described from a cold karst cave in the Irkutsk region, Siberia, Russia. It is an obligate cave species with the largest body size (4.3-5.6 mm) of all congeners. The species is further characteristic by the pseudocellar formula as 3(2)2/022/33343, high number of vesicles in postantennal organ (65-71) and subapical organite protected with two papillae. A partial sequence of cytochrome oxidase I (COI DNA barcoding marker) gene is used to verify the taxonomic status of the new species and the barcode sequence is compared with other congeners available in GenBank database. Distribution and diversity of cave Collembola of Siberia is discussed.