Determining genomic diversity, differentiation among populations and adaptation potential to a changing environment are critical elements for conservation biology of threatened, endangered and protected species. Recently, population genomic analyses based on >4000 Single Nucleotide Polymorphisms (Appleyard et al. 2021) were undertaken in one of the world’s rarest marine fish and a Tasmanian icon, the spotted handfish (Brachionichthys hirsutus). Spatially discrete populations of spotted handfish were determined in the only known estuary (in Tasmania) where multiple populations of the species are found. This insight of lower genomic connectivity in spotted handfish populations is considered alongside analyses using cutting edge Whole Genome Sequencing approaches (including Illumina short read, HiC proximity and PacBio Revio long read). In 2024, a specifically preserved spotted handfish individual underwent WGS. The population diversity and WGS analyses will provision researchers and the Commonwealth National Handfish Recovery Team with tools for informed biodiversity assessment and management of this member of the most threatened marine bony fish family.