Landscape features are effective geographical barriers resulting inpopulation differentiation of plant species. Taihang Mountains in China possess complexly geographical topology and specific landscape characteristics. Two closely related syntopic Opisthopappus species, mainly distribute in different areas of Taihang Mountains, respectively. How the landscape of Taihang Mountains affects the gene exchange between these two species still unclear. Combined SNP data from restriction-site associated DNA sequencing (RAD-seq) and recently developed landscape genetic methods (EEMS, Samβada, LFMM), we conducted a landscape genetic analysis of these two species. It found that the diversity of O. longilobus was higher than that of O. taihangensis, the gene flow was mostly from north to south along Taihang Mountains. However, a general north–south gene exchange barrier between O. longilobus and O. taihangensis was detected. Among the landscape factors of Taihang Mountains, eight was found to be the important ones, including average precipitation in August, October, and November, solar radiation in August, soil PH, built-up land, rain-fed cultivated land, and workability. And these eight factors were closely related to the occurred barriers, indicating that climatic conditions and human activities rather than geographical environment resulted in these barriers. Twenty-nine selected SNPs were identified to be significant correlated with the eight factors, especially average precipitation in November. Thus, the average precipitation in November could be regarded as an ecological indicator for O. longilobus and O. taihangensis. The results revealed the effect of landscape features on two species and the adaption on the landscape environment of Taihang Mountains during the long-term evolution.