Bacterial strain SL12-8T was characterized and isolated from the skin microbiota of Pelophylax perezi, the Perez’s frog. Strain SL12-8T stained Gram-negative and formed rod-shaped cells that grew optimally at 25 °C and pH 7.0–7.5. The G+C content of the DNA was 66.2 mol%. Ubiquinone 8 was the respiratory quinone identified in the studied strain and the most closely related taxon. The major fatty acids were summed in feature 3 and summed in feature 8 and C16:0, representing 84% of the total fatty acids. Phylogenetic analyses based on the 16S rRNA gene sequence placed strain SL12-8T within the order Burkholderiales in a distinct lineage. The 16S rRNA gene sequence similarities of strain SL12-8T to that of Rubrivivax albus, Scleromatobacter humisilvae, Piscinibacter aquaticus, Azohydromonas caseinilytica and Aquincola agrisoli were 94.41, 94.08, 93.72, 93.72 and 93.64%, respectively. The draft genome sequence of strain SL12-8T comprises 3,115,197 bases with a 313-fold mapped genome coverage. The assembled genome consists of 53 large contigs with more than 500 bp, and the genome encodes 2,814 putative coding sequences. The analysis of the available genomes from the closest genera showed 124 core genes that reveal a novel genus-level clade including the strain SL12-8T. Analysis of the SL12-8T genome revealed the presence of the beta-lactone and terpene biosynthetic gene clusters. The phylogenomic, phylogenetic, phenotypic and chemotaxonomic data showed that strain SL12-8T (=UCCCB 131T=CECT 30762T) represents the type of a novel species and genus, for which we propose the name Amphibiibacter pelophylacis gen. nov., sp. nov.