One of the introns of the phosphofructokinase gene was sequenced and analyzed in seven species of endemic Baikalian gastropods of the family Baicaliidae. The intron length differed even between sister species. Along with relatively few single nucleotide substitutions, extended deletions and insertions accumulated during the evolution of the intron. The number of deletions/insertions did not correlate with the genetic distance estimated for the species by comparing the sequences of a mitochondrial DNA fragment. The deduced secondary structure markedly differed even between sister species, although a consensus motif was detectable. Since long RNA stems that appeared and disappeared in the course of evolution may contain regulatory elements, the evolution of the intron may be nonneutral.