As marine biodiversity encounters unprecedented threats, converting high-resolution genomic data into practical management strategies is vital for effective conservation. This dissertation employs advanced genomic technologies to tackle key issues in marine biomonitoring and the spatial management of endangered species. To advance the monitoring of complex marine biological mixtures, we first benchmarked shotgun metagenomics against traditional COI metabarcoding. Using simulated and empirical multi-species fish DNA mixtures, we demonstrated that shotgun metagenomics substantially outperforms metabarcoding in quantitative accuracy by successfully mitigating severe PCR amplification biases. While its performance remains constrained by the completeness of reference databases, this approach provides a powerful, highly accurate framework for authenticating heavily processed biological materials, such as commercial aquafeed, and for advancing global biomonitoring. The subsequent chapters apply whole-genome sequencing to inform the spatial management and genetic rescue of the endangered brown sea cucumber (Isostichopus fuscus). To establish a foundational resource, we generated the first high-quality, chromosome-level reference genome for an endangered holothurian, yielding an 898.4 Mb assembly across 23 chromosomes. Leveraging this assembly, population genomic analysis of 278 individuals from the Galápagos Marine Reserve and mainland Ecuador revealed a striking departure from the expected paradigm of marine panmixia. We uncovered at least two distinct, reproductively isolated lineages coexisting in sympatry. Demographic modeling showed disparate historical trajectories with no evidence of isolation-by-distance, indicating that divergence is maintained by discrete biological barriers rather than geographic separation. Investigating the genomic architecture underlying this cryptic divergence revealed a highly decentralized, polygenic landscape supported by a widespread network of small structural variants. Notably, an ancestral, balanced inversion polymorphism was found to capture a tandem duplication of the critical lipid metabolism gene ACADL. Combined with systemic divergence in cellular division pathways, this functional convergence suggests differing physiological thresholds for reproduction, raising the hypothesis that allochronic (temporal) spawning may serve as a key isolating mechanism. Ultimately, this dissertation demonstrates the critical value of whole-genome resolution—whether for accurately quantifying complex environmental mixtures or for uncovering cryptic evolutionary units—in ensuring the sustainable management of overexploited marine resources.