This systematic review aimed to generate comprehensive information on the effectiveness of molecular markers for fish identification and conservation. Four stages were used for its execution: article identification using search directories and Boolean operators, screening all available papers, evaluating eligible articles and data extraction. Based on the analysis, mitochondrial markers, microsatellite markers, random amplified polymorphic DNA (RAPD) markers, sequence-related amplified polymorphism (SRAP) and single nucleotide polymorphism (SNP) markers are identified as the most frequently used markers. Molecular-based fish identification is the most accurate, trustworthy, reproducible and efficient technique Its effectiveness also depends on the type of molecular marker employed, the DNA sample’s quality and quantity, the fish population’s genetic diversity, the presence/absence of contaminants and the types of tissue and preservatives. The precise research topics that researchers are interested in addressing determine which molecular marker should be used.