Comparative genome mapping can rapidly facilitate the transfer of DNA sequence information from a well-characterized species to one that is less described. Chromosome arm numbers are conserved between members of the teleost family Salmonidae, order Salmoniformes, permitting rapid alignment of large syntenic blocks of DNA between members of the group. However, extensive Robertsonian rearrangements after an ancestral whole-genome duplication event has resulted in different chromosome numbers across Salmonid taxa. In anticipation of the rapid application of genomic data across members of the Pacific salmon genus Oncorhynchus, we mapped the genome of Chinook salmon (O. tshawytscha) by using 361 microsatellite loci and compared linkage groups to those already derived for a well-characterized species rainbow trout (O. mykiss). The Chinook salmon female map length was 1526 cM, the male map 733 cM, and the consensus map between the two sexes was 2206 cM. The average female to male recombination ratio was 5.43 (range 1-42.8 across all pairwise marker comparisons). We detected 34 linkage groups that corresponded with all chromosome arms mapped with homologous loci in rainbow trout and inferred that 16 represented metacentric chromosomes and 18 represented acrocentric chromosomes. Up to 13 chromosomes were conserved between the two species, suggesting that their structure precedes the divergence between Chinook salmon and rainbow trout. However, marker order differed in one of these linkage groups. The remaining linkage group structures reflected independent Robertsonian chromosomal arrangements, possibly after divergence. The putative linkage group homologies presented here are expected to facilitate future DNA sequencing efforts in Chinook salmon.