The objective of the study was to sequence the complete female mitochondrial genomes of Sinanodonta woodiana and Unio pictorum, and to ascertain their intra- and inter-specific variation within all the genes and non-coding regions. Complete sequence of maternally inherited mitochondrial genome of Sinanodonta woodiana is 16,243 bp long and is one of the three longest mt genomes in unionids; mt genome of Unio pictorum with its 15,761 bp is one of the smallest in the family. Each genome includes 14 protein-coding genes (13 as in most Metazoa, plus one open reading frame F ORF), 2 ribosomal RNA genes and 22 genes fortransfer RNA with typical secondary structures, except for tRNA for serine1. S. woodiana has 25, and U. pictorum 27 non-coding sequences, which constitute 7.8 and 4.9% of mt genome, respectively. The content of A+T bases is 65.8% in S. woodiana and 65.1% in U. pictorum; the difference between the two species is 21%. Intra-specific variation in S. woodiana is three times greater than in U. pictorum. Lower nucleotide diversity within the second species suggests a small effective population size of the Polish U. pictorum. The two species show a similar usage of the most frequent and least frequent codons; the differences pertain to the usage of both stop codons. Gene trnS1 (serine, UGA) in unionids is very little variable with respect to tRNA secondary structure (absence of DHU arm), and nucleotide composition, while its inter-specific variation is half lower than in other mt-tRNAs.