In instances of severe infestations, Nepticulidae larvae can inflict damage on cultivated plants. Previously, it was assumed that the Prunus-feeding Nepticulidae have continuous distribution from Europe to the neighboring Caucasus. During recent fieldwork in the Caucasus, leaf mines were found on plum trees that initially resembled those of Stigmella plagicolella (Stainton) in Europe. However, upon rearing the adults, significant differences emerged, leading to the hypothesis that a different Prunus-feeding species exists in the Caucasus; this challenges previous records in Western Asia. This paper presents the outcomes of our morphological, molecular, and statistical investigations, unveiling S. colchica sp. nov., a previously unknown potential plum-tree pest. Distinguished by male genitalia characteristics, the new species differs from S. plagicolella. The inter- and intraspecific divergences between S. colchica sp. nov. and S. plagicolella range from 3.5% to 6.02%. Moreover, the utilized delimitation algorithms reliably clustered two species separately, as does our mitotype network. A statistical analysis also shows a discernible trend between the leaf mines of S. colchica sp. nov. and S. plagicolella. This unexpected discovery not only documents a new potential pest, enhancing our understanding of the Caucasian fauna, but also contributes to the broader biological inventory.