The Sox9 gene of Acipenser sturio, one of the most primitive vertebrates, was analyzed. No sex-specific differences were observed. Sturgeon Sox9 consists of three exons and two introns with completely conserved exon-intron boundaries showing high levels of homology to other vertebrate Sox9 sequences, especially in the N-terminus region containing the HMG box. We found strong evidence for negative (purifying) selection. In contrast to previous studies of other fishes, we observed no evidence for gene duplication in sturgeon. Phylogenetic analyses of Sox9 evolution revealed a basal position for sturgeon Sox9.