We modified the TAR methodology of YAC clone construction for application to fish genomic DNA isolated from Xiphophorus maculatus. YAC libraries were developed using the XIR1 repeat sequence as the recombinational hook. Construction of these libraries demonstrates that Xiphophorus DNA sequences can function as hooks in the yeast recombination system and that X. maculatus genomic DNA contains sequences that provide origin of replication function in yeast. By screening a subset of Xiphophorus YAC clones, we isolated a clone harboring the Xmrk2 locus that is associated with spontaneous and induced melanomagenesis. Modifications of the TAR technique allowed the targeted cloning of specific genes from genomic regions ranging in size from cDNAs to several hundred kilobases. Specific genomic regions can be isolated in a directional manner from fixed map locations to saturate these areas with physical markers. We discuss the applications of these and other yeast recombinational processes to fish genetics.