Abstract: The Japanese anchovy (Engraulis japonicus), a keystone lipid-rich species in the Yellow and East China Seas ecosystems, plays a vital role in energy flow, and its lipid metabolism mechanisms significantly influence population dynamics. The fatty acid-binding protein (FABP) gene family is central to lipid metabolism regulation. This study aimed to systematically identify the FABP gene family members in E. japonicus and analyze their molecular characteristics and expression profiles, thereby providing a foundation for elucidating the molecular mechanisms of lipid metabolism and ecological adaptation in this species. Based on the chromosome-level genome of the E. japonicus, FABP gene family members were screened using Hidden Markov Model (HMM) and homology BLAST searches. Their phylogenetic relationships, gene structures, conserved motifs, chromosomal locations, gene duplication events, and three-dimensional protein structures were analyzed through bioinformatics approaches. Transcriptome data from different tissues (heart, liver, muscle, gonad), sexes, and body length groups were utilized to analyze gene expression profiles. A total of 14 FABP genes belonging to 7 subtypes (FABP1, FABP2, FABP3, FABP4, FABP6, FABP7, FABP10a) were identified in the E. japonicus genome, unevenly distributed across 9 chromosomes. Phylogenetic analysis classified these genes into three distinct clades. Synteny and tandem duplication analyses revealed that FABP1 genes (FABP1.1 and FABP1.2) originated from segmental duplication, while four FABP3 genes (FABP3.1-3.4) formed a tandem duplication cluster on chromosome 9. All FABP proteins possessed the typical β-barrel tertiary structure, although some FABP7 genes showed deletions of conserved motifs. Transcriptome analysis demonstrated that FABP gene expression exhibited significant tissue specificity (e.g., high expression of FABP1 and FABP10a in liver), sex specificity (e.g., specific high expression of FABP7 in testis), and certain correlations with body length. Notably, multi-copy genes (e.g., different paralogs of FABP3 and FABP7) showed markedly divergent expression patterns across tissues, suggesting potential functional differentiation. This study presents the first systematic identification and characterization of the FABP gene family in the E. japonicus. Gene duplication events, particularly the tandem duplication of FABP3, and the subsequent expression divergence may enhance the capacity for lipid uptake, transport, and utilization in E. japonicus, representing an adaptive molecular evolution in response to its high-lipid diet and periodic migratory life history. These findings provide novel theoretical insights for understanding the pivotal role of E. japonicus in energy flow within marine ecosystems at the molecular level and for the sustainable utilization of fishery resources.