The complete mitochondrial genome of sterlet (Acipenser ruthenus) was determined in this study. The mitogenome is 16,790 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 non-coding regions (the control region and the putative origin of the light strand replication) with a typical vertebrate mitochondrial gene arrangement. The overall base composition of the heavy strand is 30.26% for A, 29.00% for C, 16.23% for G and 24.51% for T, with a slight AT bias of 54.77%.