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The complete mitochondrial genomes of Brachionus manjavacas German strain were 10,721 bp (mitochondrial DNA I) and 12,274 bp (mitochondrial DNA II) in size, while the complete mitochondrial genomes of B. manjavacas Australian strain were 10,889 bp (mitochondrial DNA I) and 12,443 bp (mitochondrial DNA II) in size. Of 12 protein-coding genes (PCGs), 99.6% of amino acid sequences were identical between the two strains. Of 12 PCGs of both B. manjavacas strains, three genes (ND1, ATP6, and ND5) had incomplete stop codon T. Furthermore, ATA was the start codon for ND4, ND5, and CO3 genes, whereas that for other PCGs was ATG in both strains. The base compositions of 12 PCGs in the B. manjavacas strains were similar, indicating that the mitochondrial genome of the two strains was structurally conserved over evolution. The gene structure and its orientation of 12 PGCs of B. manjavacas strains were identical, as shown in other marine Brachionus rotifers and the freshwater Brachionus rotifers, while the freshwater rotifer B. calyciflorus had an additional cytochrome b gene in the mitochondrial DNA I.

The complete mitochondrial genome was sequenced from the NIES strain of the freshwater water flea Daphnia magna. The sequenced mitochondrial genome size of the NIES strain of D. magna was 17,432 bp, possessing identical gene order and the contents to those of the congeneric species Daphnia galeata in the genus Daphnia, but 16S and 12S rRNA genes was in opposite direction compared to other daphnid, while ND2 gene was also often found in opposite direction in the genus Daphnia. Overall, the mitochondrial genome of D. magna NIES strain has 13 protein-coding genes (PGCs), two rRNAs, and 22 tRNAs. Of 13 PGCs, four genes (CO1, CO2, ND5, and ND4) had incomplete stop codons. Furthermore, the stop codons of the remaining nine PGCs were TAG and TAA, while the start codons of CO1, ND6, and ND3 genes were ATT, ATT, and ATC, respectively. The base composition of D. magna NIES strain mitogenome shows an anti-G and –T bias (16.5% and 16.0%) on the L strand, respectively.

The two complete mitochondrial genomes were sequenced from the euryhaline monogonont rotifer Brachionus paranguensis. The mitochondrial genome sequences were 11,603 bp and 12,901 bp in size, and the gene order of 12 protein-coding genes (PCGs) were identical to those of the marine rotifer Brachionus plicatilis, but the positions of some tRNAs (e.g. tRNA-Ile, tRNA-Leu[TTA], tRNA-Phe, and tRNA-Leu[CTC]) of mitochondrial DNA I were different between B. paranguensis and B. plicatilis mitochondrial genomes. Of 12 PCGs, four genes (ND1, ATPase 6, ND5, and ND3) had incomplete stop codons. Furthermore, the start codon of ND4, ND5, and CO3 genes was ATT, while the start codon of other PCGs was ATG. The base composition of 12 PCGs in B. paranguensis mitochondrial genomes was 26.6% for A, 43.0% for T, 17.65% for C, and 12.75% for G, respectively.