Estimating biomass through quantifying egg production has become integral in the assessment and management of key fish stocks throughout the world. The Daily Egg Production Method (DEPM) is most widely used and despite its simplicity, its capability has generally been confined to species that produce eggs with distinct and identifiable morphologies. Relying on morphological criteria alone can present problems and there are examples where spawning biomass has been overestimated as a result of incorrect egg identification. Molecular validation of fish eggs and larvae is rapidly becoming an essential component of existing DEPM programs and provides a clear extension of the method to species where egg identification has been problematic. Validation methods have, so far, relied on destructive sampling, where eggs and larvae are initially identified, ascribed a developmental stage, and their DNA or RNA is chemically extracted for analysis. This process is applied to a sub-set of samples to determine a ‘correction factor’ and improve the confidence of the biomass estimate. In situ hybridisation (ISH) approaches may provide a more streamlined and non-destructive validation alternative. This involves the development of a species-specific oligonucleotide probe that targets ribosomal RNA to produce a colour reaction. Coloured eggs and larvae can then be identified under a standard stereo microscope, separated from mixed species samples, staged and archived. This study aims to investigate the feasibility of using ISH to validate snapper (Chrysophrys auratus) eggs and whole larvae from South Australian waters and subsequently extend the results to estimate the spawning biomass of this commercially important species using the DEPM.