Riccia fluitans L. is the most common species in Riccia genus. To investigate intraspecific variations on mitochondrial genomes of R. fluitans, we completed mitochondrial genome of R. fluitans. Its length is 185,640 bp, longer than that of NC_043906 by 19 bp and it contains 74 genes (42 protein-coding genes, 3 rRNAs, 28 tRNAs, and 1 pseudogene). 18 single nucleotide polymorphisms (SNPs) and 19 insertions and deletions are identified, higher than that of Marchantia polymorpha subsp. ruderalis. One non-synonymous SNP is found in ccmFN. Phylogenetic trees show that R. fluitans is clustered with Dumortiera hirsuta, requiring additional mitogenome to clarify the phylogenetic relationship.