We examined the sequence of a 2214 base pair HindIII fragment from the mitochondrial genome of six rainbow trout. The fragment encodes four proteins and two tRNAs. Sequences for two fish from a single locality were identical. Those from separate localities differed by from 1 to 7 nucleotide substitutions. Of 13 variable sites, 12 were synonymous and 1 led to a conservative amino acid substitution. Transitions accounted for 12 of the 13 variants. In contrast to interspecific comparisons (Thomas and Beckenbach. 1989. J. Mol. Evol. 29: 233-245), the intraspecific divergence estimates based on sequence are less than those estimated from restriction fragment analysis, suggesting a complex, dynamic process for the accumulation of variation in the mitochondrial genome.