Freshwater crayfish are an ecologically important group of decapod crustaceans with a vital role in freshwater ecosystems. Many of these species are, however, among the most threatened species worldwide, with declines and local extinction of many populations. Their conservation is therefore critical to mitigate the biodiversity loss and preserve the health of the entire ecosystem. Despite their important role, genomic resources are lacking due to the large and repeat-rich genomes. In this study I address this genomic gap by characterising the genome among freshwater crayfish families to inform management of threatened populations. Across Decapoda and freshwater crayfish species, I identified a large proportion of transposable elements (TE) and satellite DNA (satDNA). Freshwater crayfish species with large genomes showed a particularly large content of satDNA. Based on the analysis of TE and satDNA, I identified species-specific patterns with a phylogenetic signal. To improve repeat detection, a new annotation pipeline was developed that detected 10% more repeats than the commonly used approaches. I also propose an optimised long-read sequencing workflow based on a salting-out DNA extraction protocol combined with PacBio sequencing. A combination of amplification-based, and amplification-free library preparation strategies was used to produce high-quality long-read sequencing data sufficient for de novo assembly. Both presented methodological advancements reduce the difficulties of working with challenging genomes. I further used genomic data to inform conservation actions in the endangered Austropotamobius bihariensis. A ddRADseq dataset revealed low heterozygosity (0.149 – 0.331), few private alleles (0 – 12), and small effective populations sizes (<100) with strong structuring. Together, my results highlight the need for conservation at a population scale to maintain the unique genetic makeup and mitigate the loss of variation through drift and inbreeding in A. bihariensis. Overall, this work provides a methodological framework and understanding of generating long-read sequencing data, TEs, satDNA and genome-wide SNPs for genomic studies, comparative analyses and to translate genomic evidence into management actions for endangered species.