During a DNA barcoding campaign of leaf-mining Gracillariidae from the Asian part of Russia, a new species of Phyllonorycter Hubner, feeding on the Siberian pea shrub, Caragana arborescens Lam. (Fabaceae) was discovered in Siberia. Here, this taxon is described as Phyllonorycter ivani sp. n. Among Fabaceae-feeding Phyllonorycter, so far only P. caraganella (Ermolaev) has been known to develop on Caragana. Phyllonorycter ivani and P. caraganella show a large divergence in morphology (external and male genitalia) and barcode region of the mtDNA-COI gene (8.6%). They feed on different host plants species and have different ranges in Russia. We show that DNA barcode data weakly supports the Fabaceae-feeding species groups. In addition, we show that morphologically (strongly) and genetically (weakly), P. ivani has affinity to the haasi species group, a West Palearctic group with asymmetrical male genitalia.