Artemia is a tiny crustacean that lives in high-salinity waters and is widely distributed in inland salt lakes and coastal salt pans. Artemia is not only an important participant in the food chain of hypersaline water ecosystems, but also a crucial live food for aquatic animals. The Qinghai-Tibet Plateau is one of the regions with the most abundant salt lakes and Artemia resources in China. In recent years, the Qinghai-Tibet Plateau has experienced warming and changing precipitation patterns. Fresh water from melting glaciers and snow on the Qinghai-Tibet Plateau continuously flows into plateau lakes, leading to lake expansion and salinity reduction, which may further cause the survival crisis of Artemia in these lakes. To explore the effects of climate warming and salt lake salinity decline on the morphology and genetic characteristics of plateau salt lake organisms over the past 20 years, we selected the 1996 and 2021 Artemia populations from Lagkor Co (LGC) for culture and morphological measurement. In addition, the genetic diversity and structure of Artemia were analyzed using specific-locus amplified fragment sequencing (SLAF-seq). This study observed that although the decrease in LGC salinity in the last 25 years had negligible effect on the overall morphological changes in Artemia, the compound eye distance, second antennal length and periplieral grasping apparatus length were significantly higher in 1996 than that in 2021 (P＜0.01). A total of 229.12 Mb of read data were obtained by SLAF-seq, with an average sequencing Q30 of 92.40% and an average GC content of 36.96%. Furthermore, 263069 polymorphic SLAF tags were developed, and 680955 SNP markers were selected for population genetic analysis. Genetic diversity analysis showed that the LGC-1996 population was larger than the LGC-2021 population in E_a, O_a, and H_o indices and smaller than the LGC-2021 population in other indices; however, the overall genetic diversity difference between the two Artemia populations was small. The polymorphism information content (PIC) values for LGC-1996 and LGC-2021 were 0.268 and 0.269, respectively, indicating moderate polymorphism (0.25＜PIC＜0.5). The genetic differentiation coefficient (F_st) value between the two populations was 0.106, indicating a moderate degree of genetic differentiation (0.05＜F_st＜0.15). Phylogenetic tree analysis, principal component analysis, and kinship heat map analysis further showed obvious clustering differences between these two populations. The Admixture analysis showed that K=1 is the optimal number of subpopulations, which indicated that these two Artemia populations have differentiated to a certain extent over time, however, have not differentiated into two completely independent populations and their genetic information comes from the same original ancestor. These changes in morphological characteristics and genetic differences may be due to the decrease in salinity caused by climate warming and the genetic drift that LGC has experienced in recent years. In addition, considering the overall low level of genetic diversity and the potential threat of environmental change, developing and improving the monitoring, assessment, and protection system of Artemia resources in salt lakes of Tibet is necessary. This study not only contributes to a comprehensive understanding of the impact of climate warming on Artemia populations, but also provides theoretical support for the conservation and utilization of Artemia germplasm resources in Tibet. Key words: Qinghai-Tibet Plateau; Artemia; genetic diversity; genetic structure; germplasm resources; climate warming; saline-akali water