Black tiger prawns (Penaeus monodon) are a species of commercial importance for global aquaculture and fishery sectors. As such, efforts are underway to better understand black tiger prawn population dynamics, and enhance farming performance and productivity. Access to high quality ‘omic’ resources is vital for many of these studies, however, many resources are developed in isolation and their accuracy has not been verified. Integrating genetic linkage maps, genomes and transcriptomes allows reciprocal improvement of each resource. Here, integrating the recent P. monodon reference genome with three independent population-specific linkage maps enabled validation of the accuracy of two maps, and identified the third map was highly erroneous, despite its use in later studies. Furthermore, leveraging these validated maps, alongside raw sequencing (PacBio) and scaffolding data (HiC), the number of chromosomes was revised from 44 to 43, and misassemblies (mis-joins, mis-placements, inversions) were identified and corrected in 60% of chromosomes. Integrated genomic analysis was also applied to improve contiguity of an additional draft Australian P. monodon genome. Finally, the integrated genomic resource described within provides an improved foundation for further aquaculture and fisheries studies in P. monodon, and demonstrates the importance of such analysis for species that rely upon accurate genomic data.