Calypogeia sphagnicola is one of nine species of the genus Calypogeia known in Europe. Occurrence of the species is closely connected with peat bogs. Nowadays, two forms of this species are distinguished—C. sphagnicola f. sphagnicola and C. sphagnicola f. paludosa. The results of the present study, based on two classes of markers—isozymes and sequences of chloroplast genom (trnH-psbA, rpoC1)—unanimously support the genetic differentiation within the taxon and show that the present-day forms represent genetically distinct species. Phylogenetic analysis resolved two lineages that correspond with the present-day forms with high bootstrap support, which differ in ploidy level: C. sphagnicola f. sphagnicola is haploid, whereas C. sphagnicola f. paludosa is a diploid form. Allopolyploid origin of the diploid form was revealed by the isozyme pattern. Nei’s genetic distance between the two present-day forms of C. sphagnicola was 0.472. The forms in Poland have an allopatric pattern of geographic distribution: C. sphagnicola f. sphagnicola occurs exclusively in the lowlands of the northern part of the country on raised peat bogs, whereas C. sphagnicola f. paludosa is found only in the mountains of southern Poland, mainly in the subalpine zone, where it grows on Sphagnum-Polytrichum hummocks on the upper part of north-facing slopes. Plants regarded in this study as C. sphagnicola f. sphagnicola morphologically correspond to the syntype specimen of C. sphagnicola.