Velvet worms, Euperipatoides rowelli, are onychophorans engaged in aggregate living, collective hunting, and hierarchical feeding. Interestingly, these saproxylics display distinct phylogenetic patterns along a longitudinal gradient of semi-isolated refugia in an old growth forest the Tallaganda region in Australia. The goal of this study was to examine factors that influence gut microbial assembly and diversity among velvet worms. Using the V4-V5 region of the 16S rRNA gene, the gut microbial composition of the individual velvet worms was characterized. Interestingly, the results show low gut microbial abundance and high variability of the gut microbial communities across all velvet worm gut samples from seven localities. The dominant bacterial phyla across all samples were Actinobacteria, Firmicutes, Proteobacteria, Spirochaetes and Tenericutes. Fluorescence in situ-hybridisation did not detect bacterial signal in the velvet worm guts. Coupled with the results of feeding experiments, our findings indicate that the gut microbial communities found could be transient in nature.