We describe three new, seemingly-cryptic species in the lichen genus Caloplaca (Teloschistaceae) with black apothecia. Those species, separated in nrITS and β-tubulin DNA phylogenies, appeared to be phenotypically indistinguishable. We looked for their phenotypic differences using a two-phase method comprised of a preliminary examination in which diagnostic value of all available characters was evaluated using a small number of samples and potentially-diagnostic characters were selected, and a subsequent detailed study in which characters selected in the first phase were tested using more samples. We found 19 diagnostic characters (continuous and discrete) of which four continuous and three discrete characters could be considered “fully diagnostic”, i.e. allowing for correct identification of at least one species. Hence, the three species are not cryptic, but can be distinguished phenotypically. Here, they are formally described as Caloplaca micromarina Frolov, Khodos. & Vondrák sp. nova, C. micromontana Frolov, Wilk & Vondrák sp. nova and C. microstepposa Frolov, Nadyeina, Khodos. & Vondrák sp. nova.