Marine sponges are sources of various bioactive metabolites, including several anticancer drugs, produced mainly by sponge-associated microbes. Palk Bay, on the south-east coast of India, is an understudied, highly disturbed reef environment exposed to various anthropogenic and climatic stresses. In recent years, Palk Bay suffered from pollution due to the dumping of untreated domestic sewage, effluents from coastal aquaculture, tourism, salt pans, cultivation of exotic seaweeds, and geogenic heavy-metal pollution, especially arsenic, mercury, cadmium, and lead. Low microbial-abundant sponge species, such as
Gelliodes pumila
and
Cliona lobata
, were found to be ubiquitously present in this reef environment. Triplicate samples of each of these sponge species were subjected to Illumina MiSeq sequencing using V3–V4 region-specific primers. In both
C. lobata
and
G. pumila,
there was an overwhelming dominance (98 and 99%) of phylum
Candidatus Saccharibacteria
and
Proteobacteria
,
respectively
.
The overall number of operational taxonomic units (OTUs) was 68 (40 and 13 OTUs unique to
G. pumila
and
C. lobata
, respectively; 15 shared OTUs).
Alphaproteobacteria
was the most abundant class in both the sponge species. Unclassified species of phylum
Candidatus Saccharibacteria
from
C. lobata
and
Chelotivorans composti
from
G. pumila
were the most abundant bacterial species. The predominance of
Alphaproteobacteria
also revealed the occurrence of various xenobiotic-degrading, surfactant-producing bacterial genera in both the sponge species, indirectly indicating the possible polluted reef status of Palk Bay. Studies on sponge microbiomes at various understudied geographical locations might be helpful in predicting the status of reef environments.