This entry contains raw sequence data of the microbial community associated with the soft coral Lobophytum pauciflorum generated with Illumina MiSeq (16S rRNA gene amplicon). The microbial community of L. pauciflorum was dominated by Spriochaetes and Endozoicomonas. At class level no difference between male and female colonies was detected. Exposure of soft coral fragements to increased temperature (31 °C), decreased pH (7.9) or both stressors simultaneously for 12 days did not significantly alter the microbial community, indicating that the soft coral microbiome is stable and resilient to short term environmental stress.