FASTA file with the sequences for amphibian, fish and reptile species registered to occur in Mexico City, functioning as a custom reference database for the 12S-V5 metabarcoding library. The Alt12S primer pair was developed for the project, yielding amplicons that contain the MiFish and 12S-V5 markers. Sanger sequences were obtained through DNA extractions from preserved tissues (obtained through the project's collaborators) using the QIAGEN DNeasy Blood & Tissue kit. The processing of the sequences (including de novo assembly) was done using Geneious Prime. Sequences were used during the Taxonomy Assignment step of the bioinformatic pipeline using Python packages BLAST+ and BASTA.