Genetic diversity is a key factor in determining the adaptive potential and resilience of fish populations to environmental stressors. This review aimed to evaluate existing research on the molecular genetic diversity of Nigerian fish populations, with a focus on species studied, geographical coverage, and methodological approaches. The goal was to assess the suitability of these studies and identify knowledge gaps to guide future research and improve the monitoring and conservation of fisheries resources in Nigeria. A total of 42 relevant articles were retrieved from three academic databases following a screening process using predefined inclusion and exclusion criteria. The earliest study recorded (based on the selected databases and the search terms) was published in 2011, with a noticeable increase in publications over time. Approximately 70% of the studies focused on fish populations from the Southwest and South-South regions of the country. Inland water bodies and aquaculture environments accounted for 64% of the study settings. Taxonomically, catfishes and cichlids were the most frequently studied groups, with Clarias gariepinus representing nearly 60% of the catfish-related studies. The most commonly used molecular markers were mitochondrial DNA (mtDNA), simple sequence repeats (SSR), and randomly amplified polymorphic DNA (RAPD), with an average loci per population of 1.4 loci (mtDNA), 6.55 loci (SSR), and 5.14 loci (RAPD), respectively. The review highlighted the limited effectiveness of mtDNA for comprehensive genetic diversity assessments due to its narrow genomic coverage. It recommends the adoption of more robust molecular tools, particularly next-generation sequencing (NGS) technologies such as single nucleotide polymorphisms (SNPs). Furthermore, integrating landscape level environmental data into population genetic studies is suggested to enhance the understanding and management of Nigeria’s fish genetic resources.