In the Pirin Mountains, at an elevation of around 1000 m, three populations of a new species of Bulgarian flora from the genus Crocus, series Verni, were discovered. The species was compared to the morphologically related C. veluchensis, and presented with diagnostic morphological and anatomical features. Despite the high degree of morphological similarity, the molecular analysis, which included sequences from all related species (C. cvijicii, C. dalmaticus, C. jablanicensis, C. rujanensis, C. sieberi subsp. atticus, and C. veluchensis), distinguished the Pirin Mountains’ populations, and revealed the closest relationship to C. heuffelianus. Despite the C. heuffelianus/C. verni complex’s uncertain taxonomic status, our findings on the local population, based on morphometric, anatomical, molecular, and geographic analyses, indicate its belonging to the putative allotetraploid C. heuffelianus of south-eastern Europe and the Balkans, and an expansion of its range to the southeast. Given the taxonomic uncertainty and unclear phylogenetic relationships of the taxa in the Crocus vernus complex, we considered it appropriate to accept our taxon as Crocus heuffelianus. So far, only C. tommasinianus Herb. has been found in Bulgarian flora from the Crocus series Verni, but in terms of altitude and morphological features, the species from our collection is close to the Balkan endemic C. veluchensis, which belongs to the C. sieberi aggregate. Morphologically, it differs by the dark, heart-shaped spots on the tip of the tepals, and the presence of one bract. A detailed comparative anatomical analysis between the three species of crocuses from the series Verni in Bulgaria shows discrete differences: the width of the white stripe and lacunar area are good distinguishing features, as are the number of conducting vessels.