ddRADseq data from a single 300 cycle NextSeq run using a high-output kit.Raw sequence data with barcodes required to demultiplex. Contains 38 individuals: two Hypogeophis montanus, 3 H. brevis, 5 H. sechellensis and 4 each of H. pti, H. larvatus, H. alternans, H. rostratus, Praslinia cooperi, Gegeneophis ramaswamii and Idiocranium russeli.Phylip format alignments with variable sites only. Filtered for between 0 and 80% maximum missing data per locus, minor allele count of 2, minimum read depth 2 and minimum read quality of 30. Includes the final alignment used in the study with 50% missing data allowed 'filtered_mac2_minq30_missing50_minDP2.varsites.phy'. Contains 37 samples from the caecilian species Hypogeophis montanus, Hypogeophis pti, Hypogeophis brevis, Hypogeophis sechellensis, Hypogeophis larvatus, Hypogeophis rostratus, Hypogeophis alternans, Praslinia cooperi, Gegeneophis ramaswamii and Idiocranium russeli.