The genus Choeradoplana encompasses 11 species, nine of which have a restricted distribution and are only known from their type localities. Herein we describe two new species of Choeradoplana from Araucaria moist forests, C. minima, sp. nov. Lemos & Leal-Zanchet and C. benyai, sp. nov. Lemos & Leal-Zanchet, based on morphological and molecular data, and use two molecular markers to investigate their phylogenetic relationships with other species in the genus, including its type species. Both morphological and molecular analyses clearly distinguish C. minima, sp. nov., C. benyai, sp. nov. and C. iheringi. The analyses of the ITS-1, COI and sequence divergence data also indicated that C. benyai, sp. nov. is more closely related to the type species of the genus, C. iheringi, than to C. minima, sp. nov. The three species are sympatric in Araucaria moist forest areas of the São Francisco de Paula National Forest; C. minima, sp. nov. and C. benyai, sp. nov. seem to be endemic to their type localities. Regarding external morphology, C. benyai, sp. nov. and C. iheringi could be considered cryptic species, only distinguishable on the basis of the copulatory apparatus. However, immature specimens of C. benyai, sp. nov. and C. iheringi could only be identified based on molecular data. Our results demonstrate that COI should be used with caution for reconstructing phylogenies, and other slower-evolving nuclear genes are a feasible alternative for resolving some of the phylogenetic relationships.