Rhagoletis merzi sp. n., is described and illustrated based on specimens swept and reared from Juniperus sabina L. in Switzerland. A comparative review of Palaearctic species and a key to Palearctic and Nearctic species similar to R. merzi is provided. Based on DNA sequences from the COI, CAD, 28S, period, and AATS genes (4270 bp) of 92 isolates from two outgroup species (Anastrepha ludens, Euphranta canadensis), one species of Carpomya and 35 species representing most of species groups of Rhagoletis, a MrBayes analysis recovered a monophyletic lineage of Juniper-infesting species within a monophyletic cluster of R. fausta, R. batava, as well as the suavis, cingulata, pomonella, tabellaria and juniperina groups.