We report the development of more than 250 informative microsatellite markers, and the first stage of construction of a comprehensive microsatellite-based genetic linkage map for the saltwater crocodile (Crocodylus porosus). This map represents the first genetic linkage map in the Order Crocodylia and indeed the first in the Class Reptilia. These markers will be used to map Quantitative Trait Loci (QTL) for economically important selection objectives in farmed saltwater crocodiles. Any QTL identified may then be useful in implementing a Marker-Assisted Selection (MAS) genetic selection program. High-density genetic maps for QTL identification require many polymorphic markers spaced evenly across the genome. Our map, which we anticipate completing by mid-2007, will contain approximately 300 informative genetic markers selected from more than 600 microsatellites that were originally developed and evaluated. The 600 loci will be evaluated for utility in all extant crocodilian species for future research.