The overall goal of this research project was to determine optimal strategies for applying genomic mapping, quantitative trait loci (QTL) detection and marker-assisted selection (MAS) to genetic improvement of aquaculture species. Genes affecting aquaculture performance, or quantitative trait loci (QTLs}, can be mapped in relation to naturally-occuring genetic markers. Knowledge of linkages between marker and QTL alleles can be used for marker-assisted selection (MAS), potentially increasing the rate of genetic progress above that for selective breeding alone. QTL detection and MAS have not yet been practiced on an aquaculture species. I reviewed the technical literature on QTL detection and MAS in other species in order to advance critical discussion of how best to pursue QTL detection and MAS in fish. The need for cost-effectively screening markers suggests polymerase chain reaction-based screening of a collection of microsatellite loci or RAPDs (random amplified polymorphic DNAs). Experimental power calculations suggest that because markers will have to be screened within large progeny groups, selective or sequential genotyping or screening of bulked DNA samples will be needed for costeffective detection of QTLs. DNA amplification fingerprinting (DAF) profiles were generated for brook trout, Salvelinus fontinalis, in an attempt to identify a genetic marker for the sex determining locus. DNA mixes of nine males and nine females from a group of closely related fish were screened with 100 arbitrary decamer primers to identify candidate markers for more detailed analysis. Upon screening a panel of three male and three female individuals, however, none of the candidate markers proved to be strictly associated with one sex or the other. Screening of DNA rnicrosatellite loci was used to construct a genomic map for tilapia (Oreochromis sp). A male hybrid between Oreochromis aureus and red O. niloticus was crossed with a female O. mossambicus to produce the 3-way cross mapping family. A panel of DNA samples of 2 grandparents, 2 parents and 60 F2 individuals was screened for microsatellite markers with 133 primer pairs using polymerase chain reaction. The genetic map I produced consists of 22 microsatellite loci placed into two linkage groups, with 17 loci remaining unlinked. The microsatellite data were integrated with amplified fragment length polymorphism (AFLP) data from collaborators to construct the overall linkage map with 191 markers in 25 linkage groups. / Ph. D.