Comparative genomics is a powerful tool to transfer genomic information from model species to related non-model species. Channel catfish (Ictalurus punctatus) is the primary aquaculture species in the United States. Its existing genome resources such as genomic sequences generated from next generation sequencing, BAC end sequences (BES), physical maps, linkage maps, and integrated linkage and physical maps using BES-associated markers provide a powerful platform for comparative genomic analysis. Based on this platform, this study aimed to gain understanding of similarities and conserved syntenies between the catfish genome and model teleost fish species genomes by examining linkage group 28 (LG28). A total of 368 unique genes were identification in LG28 by BLAST. The genomic locations of the genes with significant unique hits were determined and comparative maps were constructed using AutoGraph. The genes on catfish LG28 are mostly located on zebrafish chromosomes 7 and 2 with 154 unique hit genes on chromosome 7 and 88 unique hit genes on chromosome 2; Similarly, the genes on catfish LG28 are mostly located on medaka chromosome 18, 17, and 20, with 99, 59, and 31 unique hit genes, respectively; and on stickleback chromosomes 7, 3, and 21 with 81, 62, and 31 unique hit genes, respectively; and on Tetraodon chromosomes 15, 20, and 6, with 51, 26, and 19 unique hit genes, respectively. These results suggested the presence of many conserved syntenies but also intense rearrangements of chromosomal segments through evolution. It is interesting to observe a higher level of genome scale structural conservation between catfish and zebrafish than between catfish and the other three fish species. Ongoing research is focused on establishing orthogues, conserved syntenies, duplicated genes, and functional annotation of genes on LG28.