Riccia fluitans L. (Marchantiales) is an aquatic liverwort usually found in lentic environments. Here, we presented a complete chloroplast genome of R. fluitans (MK645896) which is 121,682 bp long and has four subregions: 81,626 bp of large single copy (LSC) and 20,254 bp of small single copy (SSC) regions are separated by 9,901 bp of inverted repeat (IR) regions including 131 genes (87 protein-coding genes, 8 rRNAs, and 36 tRNAs). The overall GC content is 29.0\% and those in the LSC, SSC, and IR regions are 26.6\%, 24.6\%, and 42.9\%, respectively. Phylogenetic trees show incongruence with Bryophyte taxonomy, requiring intensive researches to find genes causing this incongruence.