The Australian National Fish Collection (ANFC) holds over 150 000 specimens representing approximately 3 400 species mostly collected from the Indo-Pacific. Its strengths are sharks, rays and deep-water fishes. Alongside taxonomy, genetic/genomic research in the ANFC focusses on species identifications, phylogenetics, biogeography, population connectivity and inputs into sustainable fish management and conservation. These research activities have been improved due to our involvement as an integral partner in several domestic and international barcoding and next generation sequencing consortia. As part of these consortia, genetics/genomics in the ANFC is divided into two equally important components – a. taxonomic validation and uptake of mtDNA barcoding for reference databases to enable rapid species identifications, informed phylogenetic analyses and increased species discovery; b. detection of new nuclear genomic regions of interest for species of commercial and biodiversity importance using next generation sequencing. This presentation is a reflective synopsis of our experiences with genomic investigations in fish. Extensive data sets and numerous case studies ranging from the application of alternate sequencing approaches and the manipulations of large data sets in "the cloud" to the judicious choice of molecular tools to address the question in hand will be presented. These data sets act as references for discovery and understanding of Australian fishes, including improved resolution of taxonomic structure, distributional ranges and habitat preferences.