Background/Objectives: Desert plants exhibit remarkable resilience to extreme environments, and their capacity for population establishment is noteworthy. However, the adaptation process mechanisms of those plants to harsh habitats, particularly concerning intraspecific differentiation and genetic diversity, remain poorly understood, and a comprehensive framework is lacking. Zygophyllum loczyi Kanitz, an annual or biennial desert herb, demonstrates significant phenotypic plasticity across diverse habitats. Methods: Using mixed-effects models, this study examined 20 populations from four deserts to assess phenotypic variation and predict trait_environment relationships. Results: The findings indicated substantial inter-population phenotypic differentiation in Z. loczyi, with greater variation observed between deserts than within them. Traits such as blade length, petal length, sepal length, and stamen length were influenced by environmental conditions. Mixed-effects model prediction showed that the growth location of Z. loczyi significantly impacted its phenotypic traits. The characteristics of the four desert populations displayed varying responses to temperature and moisture changes, with the most pronounced response noted in the Gurbantunggut desert (Gt) population, indicating that survival stress has an important influence on the performance of plants. The single nucleotide polymorphisms result further confirmed that the differentiation and genetic diversity of the Gt population displayed the highest selection pressure, resulting the small effective size of the population. Conclusions: This study uncovers the adaptive mechanism of Z. loczyi to habitat through investigating the inter-population phenotypic differentiation and genetic diversity and provides new insight into local adaptation and evolutionary processes in the desert environment.

Ammopiptanthus nanus, a Tertiary-era endangered plant, is of great scientific value. In this research, we focus on A. nanus population dynamics in an effort to bridge the divide between micro genetic variation and a macroscopic ecological pattern of distribution. The population structure of 129 wild specimens of A. nanus from eight populations was analyzed using EST-SSR molecular markers in this research. The Mantel test and RDA analysis have been used in this research to investigate the factors that influence the genetic diversity of A. nanus. Using 15 pairs of SSR primers, a total of 227 alleles were detected in 129 samples from 8 populations. The mean number of alleles was 17, and the average expected heterozygosity was 0.405. It is shown that wild A. nanus is divided into six individual populations. A. nanus are significantly affected by wind speed in terms of the variation of genetics. It is suggested that a nature conservation area for A. nanus be established as soon as possible, based on our results and the current natural distribution of the species. It is necessary to focus on the issue of pests and diseases while simultaneously preventing the continuation of anthropogenic woodcutting and disaster. Manual seedling collection should be employed in regions where the environment permits. Through making use of manual breeding techniques, this will contribute to the growth of the natural population of A. nanus.