Red chilli pepper (Capsicum annuum; RP) is a popular spice containing the active compound capsaicin. Indigenous gut bacteria and metabolism can affect host health. The functions of capsaicin, including the regulation of metabolic health and anti-oxidant properties, may be correlated with the gut microbiota. To identify indigenous gut bacteria that are responsive to RP, Institute of Cancer Research mice fed a diet with no fibre or with 5% (w/w) RP for 14days. Additionally, human stool samples collected from four healthy volunteers were incubated without (control) or with 2% (w/v) RP at 37°C for 24h. Microbiota in murine caecal samples and human faecal cultures were analysed using 16S rRNA (V4) amplicon sequencing. Compared with the microbiota in mice fed no-fibre diets, Lachnospiraceae spp.-, Muribaculaceae spp.-, and Phacaeicola vulgatus-like bacteria were defined as murine RP-responsive indigenous gut bacteria (RP-RIB). In the human faecal cultures, acetate and propionate levels were higher in RP cultures than in the control cultures. Subdoligranulum spp.-, Blautia spp.-, Faecalibacterium prausnitzii-, P. vulgatus-, and Prevotella copri-like bacteria were defined as human RP-RIB. Compared with control culture Fe-reducing power was increased in the culture with RP. RP increases the amount of short-chain fatty acid-producing bacteria and beneficial gut bacteria in mouse and human faecal cultures. Overall, RP could have a positive effect on the host by altering the gut microbiota.