The phylogenetic relationships of the monospecific genus Paratricharia, with the single species P. paradoxa, within the family Gomphillaceae are resolved using newly generated sequences of the mtSSU and nuLSU markers for three specimens collected in Costa Rica. The results support placement as sister to the genus Caleniopsis, the two genera sister to a clade containing the genera Aulaxina and Aulaxinella. This placement confirms earlier studies based on cladistic analysis of phenotype characters and phenotype-based phylogenetic binning, suggesting that apothecial features are more informative for the phylogenetic placement of taxa within Gomphillaceae than thallus characteristics.