Abstract: 【Objective】 To screen differentially expressed proteins（DEPs） in gill tissues of low temperature sensitive and tolerant GIFT tilapia（Oreochromis niloticus）, which could provide theoretical basis for exploring the molecular mechanisms of low temperature tolerance in tilapia, and offer basic genetic data for breeding new low temperature resistant GIFT tilapia varieties（lines）. 【Method】 Isobaric tags for relative and absolute quantification（iTRAQ） technology combined with liquid chromatography-tandem mass spectrometry（LC-MS/MS） were used for proteomic analysis of gill tissues from GIFT tilapia before and after low temperature stress. DEPs were screened based on the criteria of Fold Change＞1.3 and P＜0.05, followed by GO functional annotation, KEGG signaling pathway enrichment analysis, and validation via real-time fluorescence quantitative PCR（qRT-PCR）. 【Result】 A total of 6603 proteins were identified, including 746 DEPs（432 up-regulated and 314 down-regulated）. GO functional annotation analysis showed that 746 DEPs were annotated to 4772 GO terms across 3 functional categories: biological process（BP）, cellular component（CC） and molecular function（MF）. KEGG signaling pathway enrichment analysis revealed that 746 DEPs were enriched in 31 subgroups of 5 KEGG pathways categories, with 115 DEPs（15.4%） in the immune system, 88 DEPs（11.8%） in signal transduction, and 75 DEPs（10.1%） in global and overview maps. In terms of enrichment degree, 746 DEPs were mainly enriched in 15 KEGG signaling pathways such as the intestinal IgA immune network, hematopoietic cell lines, ribosomes, complement and coagulation cascade response. qRT-PCR results showed that multiple key genes including C3 and C5 were greatly down-regulated in gill tissues of low temperature tolerant GIFT tilapia, especially the expression of C1qrs, CD59, C3, C5, C6 and Vtn genes extremely significantly down-regulated（P＜0.01）. 【Conclusion】 After low temperature stress, DEPs in gill tissues of GIFT tilapia are mainly enriched in pathways related to specific/non-specific immunity, carbohydrate metabolism, and lipid metabolism, such as intestinal IgA immune network, hematopoietic cell line, complement and coagulation cascade response. The suppression of the fish immune system and the decline in resistance to external adverse factors are the main causes of mass mortality in tilapia under low temperature stress.