The bean bug Riptortus pedestris develops numerous sac-like tissues called crypts at the posterior region of the midgut, wherein a Burkholderia symbiont is fully colonized. In this study, we performed RNA-sequencing (RNA-seq) of symbiont cells colonized in the insect midgut (in vivo) and cells cultured by YG medium (in vitro). For in vivo samples, total RNA was extracted from midgut crypts pooled in 10 to 30 insects, and in total three pooled samples were purified by Eukaryote Ribo Minus (-E) kit and/or Bacteria RiboMinus (-B) kit. For in vitro samples, total RNA was extracted from 2 independent samples of overnight culture. One sample was purified by Bacteria RiboMinus (-B) kit, but the other was not. We analyzed three replicates for in vivo cells (M4-E1, M4-E2, M4-E-B) and two for in vitro cells (Cultured0, Cultured0-B).