The smooth newt (Lissotriton “Triturus” vulgaris) and Montandon’s newt (L.“T.” montandoni) are sister species exhibiting pronounced differences in male secondary sexual traits but nevertheless hybridizing and producing fertile hybrids in nature. Since pheromonal communication is an important aspect of the reproductive biology of urodeles, structural differentiation of peptide pheromones and their receptors may contribute to incipient reproductive isolation. The aim of the study was the identification of genes encoding putative courtship pheromone precursors in two newt species and the reconstruction of phylogenetic relationships among them. Our analyses were based on cDNA obtained from the transcripts from the abdominal glands of male newts. We identified five unique cDNA sequences encoding the putative pheromone precursors in L. vulgaris and three additional unique sequences in L. montandoni. The results indicate that in the abdominal glands of Lissotriton newts more than one pheromone-encoding gene is expressed and that these loci form a gene family. Phylogenetic analysis indicates that the divergence of at least some of these genes predates the radiation of European newts.