Abstract: 【Objective】 This study aimed to reveal differences in gene expression and metabolic pathways between female and male Onychostoma gerlachi through transcriptomic analysis, which could provide reference for the exploitation and utilization of its germplasm resources. 【Method】 Transcriptome sequencing of mixed brain, liver, and muscle tissue samples from adult female and male Onychostoma gerlachi was performed using the Illumina Hiseq^TM 2000 platform. After quality control and assembly, unigenes were functionally annotated against the Nr, COG/KOG, KEGG and SWISS-PROT databases. Differentially expressed genes（DEGs） were screened using thresholds of FDR≤0.05, |log₂ Fold Change| ≥1 and P＜0.05. Biological functions and metabolic pathways of DEGs were analyzed via GO functional annotation and KEGG pathway enrichment. SSR loci were identified using MISA. 【Result】 Transcriptome sequencing of 6 Onychostoma gerlachi tissue samples generated 59628 unigenes, with N50 length of 2209 bp. The annotation success rate across Nr, COG/KOG, KEGG and SWISS-PROT databases was 55.82%, with Nr annotating the most unigenes（33201）, and 71.06% annotated genes was homologous to zebrafish. A total of 3116 DEGs were identified between male and female Onychostoma gerlachi: 2254 down-regulated and 862 up-regulated. Among the top 10 up-regulated DEGs, 4 were unannotated and exclusively expressed in male samples. DEGs were primarily enriched in GO terms including biological process, metabolic process, cellular process, binding and catalytic activity. KEGG metabolic pathways enrichment revealed 614 DEGs enriched to 158 pathways, covering lipid metabolism, amino acid metabolism, carbohydrate metabolism, endocrine system, and transport/catabolism. A total of 12012 SSR loci were screened out from the transcriptome of Onychostoma gerlachi, among which dinucleotide type SSR loci were the most numerous（6740）, accounting for 56.11%. 【Conclusion】 There are a large number of DEGs in the transcriptomes of female and male Onychostoma gerlachi, which leads to ob-vious differences in the utilization ability and strategies of different nutrient metabolisms between female and male indivi-duals, with females exhibiting potentially higher metabolic activity. Thus, future research on growth performance and stress resistance in Onychostoma gerlachi should consider sex-specific metabolic variations.