Animal-associated microbiomes play an important role in metabolic activities including immune functions of hosts. Microbiome related work, facilitated by next-gen approaches are now emerging for amphibians, but the microbiome of caecilians that constitute of 3% of the amphibians are unknown. Here we explore the gut and skin microbial diversity of larval caecilians. We used 16S rRNA gene amplicon sequencing to evaluate the bacterial communities present in the gut and skin samples of larval Ichthyophis bannanicus (n = 13), a common caecilian distributed across South-East Asia. Our studies showed that gut and skin bacterial communities included Bacteriodetes, Proteobacteria, Firmicutes, Verrucomicrobia, and Actinobacteria at the phylum-level core microbiome, though the percentage of the bacterial phyla were significantly different between gut and skin samples. The similarity between the gut and skin may be attributed to the life history stage. The microbiome at phylum level in anurans (frogs and toads) is known to consist of mainly Proteobacteria, Fusobacteria, Firmicutes, Bacteriodetes and Cyanobacteria. Proteobacteria are thought to play key role in preparing the gut for colonization by anaerobes required for healthy gut function by consuming oxygen, and lowering redox potential in the gut environment. Bacteriodetes perform metabolic conversions that are needed for the host such as degradation of proteins or complex sugar polymers. Data for caudate (salamanders and newts) larvae is absent. However, it appears that larvae of different orders of amphibians have distinct bacterial phyla.