Several species of Centrophorus have been harvested beyond sustainable limits in the Pacific, Atlantic, and Indian Oceans. Effective monitoring of current recovery plans in Australia requires the implementation of a catch data verification plan. The utility of the 16S mitochondrial gene region was evaluated for discriminating among seven recognised morphologically similar Centrophorus species caught in commercial fisheries in Australia and Indonesia. The 16S gene amplified consistently, was sequenced in all individuals tested, and was able to distinguish all species with sufficient resolution for routine testing, apart from C. harrissoni and C. isodon. These two allopatric species were distinguishable using four types of external morphological characters. We conclude that the 16S gene is a robust marker suitable for fishery catch verification of Centrophorus, particularly for Australian samples collected under non-ideal conditions for preservation. When combined with morphological characters, this approach is a reliable and efficient system for routine testing. Trials with the CO1 mtDNA gene found that specialised primers are needed; trials with the Cytb mtDNA gene found this marker is sensitive to preservation problems. Future development of the 16S and CO1 markers are likely to contribute to resolution of taxonomic problems within the Centrophoridae.