The main objective of this project was to generate a large single nucleotide polymorphism (SNP) marker resource for later saturation of the genetic linkage map and fine mapping of quantitative trait loci (QTL). Another objective of this project was to learn more about basic crocodile biology, namely immune function and stress, and the underlying genetic function to evaluate their incorporation into CrocPLAN. This report describes the development of new phenotypic trait panels for farmed saltwater crocodiles. Among these is the major crocodilian stress hormone, corticosterone (CORT), which should be useful for the development of animal welfare standards and the eventual selection of individuals in the future. Immune assays, some of which have never been previously used in crocodilians, were employed in this project to assess immune function. These immune assays, which are relatively easy to perform and cheap, could be employed in any farming setting to assess immune function in the future. Levels of estradiol (ESTR) and testosterone (TEST) are also detailed in this report, for the first time in the saltwater crocodile. At the same time as trying to expedite industry adoption of genetic improvement programs, it was necessary to expand on the current selection criteria available to gain a deeper insight into the breeding objectives already defined from RIRDC Project US-109A. The traits added were corticosterone (the main crocodilian stress hormone), two immune parameters, two sex hormones (testosterone and estradiol), two behaviour characters and four skin quality traits. Simultaneously, some of these traits could be used to gauge current industry practices which are set out in the “Code of Practice on the humane treatment of wild and farmed Australian crocodiles”. I am pleased to report that the lowest levels of corticosterone ever reported in saltwater crocodiles were found certifying the recommendations set out in the “code of practice”.