Foam nest construction is a unique oviposition method that evolved independently in anurans lineages from the Neotropics, Asia, and Africa. The nest’s formation involves protein secretions from the oviduct follow by a series of fast kicking of the hind legs by the amplectant pair. One of their potential functions is protection against pathogens, but with a lack of supportive evidence. In this sense, the overall aims of our project is to understand whether skin’s antimicrobial peptides (AMPs), produced by dermal glands may be incorporated to the foam during nest formation and modulate its microbiome. This study represents the first steps on this regard. Here, we analyzed transcriptomes from dorsal skin region of a male and a female of Physalaemus santafecinus to assess AMP gene expression. To assemble the transcriptome, we used Trinity and Spades, and Transdecoder and Orfpredictor for translation. Using conserved sequences from the signal peptide region of described prepro-peptides in amphibians, over 40 mature peptides were found in male, 37 in the female, and only 2 in oviduct. The two peptides expressed in the oviduct were also present in skin of both sexes. More than 10 peptides were expressed in both sexes, and other several exhibited similar sequences. These are newly described peptides, sharing <50% similarity with the 3569+ AMPs in the APD (Antimicrobial Peptide Database). Physicochemical analysis revealed varied charges, hydrophobicity, and 3D structures. This transcriptomic characterization of Physalaemus santafecinus skin, coupled with biochemical and microbiological data, offers crucial insights into reproductive mechanism and the role of secretions in foam nest construction.