An in-depth investigation into wild L. pumilum was conducted in Taigu, Jinzhong City, Shanxi Province. This study, for the first time, clearly delineated the distribution, germplasm diversity and the pattern governing flower color differentiation of L. pumilum in Taigu. Preliminary investigations were conducted into the genetic underpinnings and molecular mechanisms that drive flower color variation among wild L. pumilum populations in Taigu. These variations were evaluated from phenotypic, cytological, physiological and molecular perspectives. The results showed that L. pumilum in Taigu is distributed within a longitude range of 112° 39′ 50″ to 112° 95′ 64″, a latitude range of 37° 19′ 12″ to 37° 42′ 17″, and an altitude range of 963 m to 1430 m. Notably, L. pumilum was absent from Xiaobai, while 683 plants were found in Yangyi, 394 in Fancun and 246 in Houcheng, totaling 1323 plants. Phenotypic diversity of L. pumilum is evident in plant height, stem color, flower color, hairy flower buds and seed color. The diversity in plant height is significantly correlated with altitude, whereas the diversity in flower and stem color was significantly correlated with geographical distribution of the plants. Using a color card and colorimeter, the five flower colors of L. pumilum were identified as orange, orange red, red, dark red and purple red. Orange red was the most abundant color, accounting for 90.2% of the population. Xiaodian and Yangyi are the only locations where all five flower colors coexist. The color differences among these five flower colors are pronounced, with orange and orange red L. pumilum being the most vivid. Carotenoids in the plastids serve as the primary coloring substances found in L. pumilum. The varying carotenoid content in the upper and lower epidermis leads to changes in flower colors between orange, orange red and red varieties. In contrast, the dark red and purple red colors of L. pumilum are due to the carotenoids being largely obscured by anthocyanins present in the vacuoles. Expression analysis of genes involved in the anthocyanin biosynthesis pathway suggests that LpDFR and LpbHLH2 may be the key genes responsible for this color differentiation observed in L. pumilum flowers. This study provides a theoretical foundation for the formulation of protection and innovative utilization strategies for L. pumilum germplasm resources. Additionally, it offers potential germplasm resources for genetic improvement and the cultivation of new varieties of L. pumilum.