Zebra mussels Dreissena polymorpha (Veneroida, Dreissenidae) are known for their invasive behavior. Despite numerous studies dealing with this species, no results of large sequencing projects have been published to date, hampering marker development. In this study, we present a relatively large novel transcriptomic dataset obtained by Illumina MiSeq technology from mantle and male gonad of D. polymorpha sampled in Poland. The transcriptomic data were typical for the tissue analyzed. Moreover, they showed the expression of a single mitochondrial genome, indicating that this species do not have doubly uniparental inheritance of mitochondria. The sequences of mitochondrial transcripts were used to design primers and obtain nearly complete sequence of the zebra mussel mitochondrial genome by PCR and Sanger sequencing. This mitogenome has unique gene order, with the genes split into two blocks encoded in opposite directions. The closest mitogenome available in GenBank belongs to the marine clam Mya arenaria (Myoida, Myidae). The average divergence of the sequences of these mitogenomes is quite high, in the range of 20%. Both mitogenomic and transcriptomic resources should prove very useful for elucidating population genetics and conservation issues involving this important species.