Ironwood trees (Casuarina equisetifolia) in Guam have been suffering from Ironwood Tree Decline (IWTD) since 2002. Putative plant pathogenic bacteria such asRalstonia solanacearumandKlebsiellaspecies were identified in the ooze of declining trees and considered to be linked to IWTD. In addition, termites were found to be significantly associated with IWTD.Microcerotermes crassusSnyder (Blattodea: Termitidae) was identified as a termite species that attacks ironwood trees in Guam. Since termites harbor a diverse community of symbiotic and environmental bacteria, we sequenced the microbiome ofM. crassusworkers attacking ironwood trees in Guam to assess the presence of IWTD-associated pathogens in termite bodies. This dataset contains 652,571 raw sequencing reads present inM. crassusworker samples collected from six ironwood trees in Guam obtained via sequencing the V4 region of the16S rRNA gene on the Illumina NovaSeq (2 × 250bp) platform. Sequences were taxonomically assigned in QIIME2 using SILVA 132 and NCBI GenBank as reference databases. Spirochaetes and Fibrobacteres were the most dominant phyla inM. crassusworkers. No putative plant pathogens of the generaRalstoniaorKlebsiellawere found in theM. crassussamples. The dataset has been made publicly available through NCBI GenBank under BioProject ID PRJNA883256. This dataset can be used to compare the bacterial taxa present inM. crassusworkers in Guam to bacteria communities of related termite species from other geographical locations. In addition, this dataset can also be used to investigate the relationship between termite microbiomes and the microbiomes of ironwood trees they attack and of the surrounding soil.