Hemp (Cannabis sativa L.) is an annual, and dioecious herb belonging to the Cannabaceae family. This plant is native to Central and Southeast Asia. The wild races of this species are commonly growing in Khyber Pakhtunkhwa and Punjab provinces, as well as in Islamabad, Pakistan. This study provides crucial insights into how environmental variables influence the wild hemp populations, which can be utilized in for conservation and breeding. The present study was aimed at evaluating the effects of key environmental factors such as altitude, geographical location, precipitation, relative humidity, maximum, minimum, and average temperature on 16 morpho-agronomic traits of a wild population of hemp growing in the Potohar Plateau and Lesser Himalayas. Our findings indicated that high relative humidity (> 64%), low average temperature (< 15 °C), intermediate average temperature (19–22 °C), and high average temperature (> 22 °C) played significant roles in determining the distribution pattern of the wild hemp. Correlation analysis demonstrated that average annual temperature contributed a higher percentage of variation in phenotypic diversity than geographic variables. Additionally, cluster analysis indicated three groups for the selected 35 populations. Clustering and Principal Component Analysis (PCA) of the morpho-agronomic traits indicated that group 1 from the Lesser Himalayas showed high relative humidity (> 64%) and low average temperature (< 15 °C). Conversely, Group 2 populations from the Potohar Plateau demonstrated intermediate average temperature (19–22 °C). There is an existence of Group 3 in the Potohar Plateau with a high average temperature (> 22 °C) compared to Group 1 and Group 2. Our examination highlights the complex interplay between ecological factors, and morphological attributes in native landraces of Cannabis sativa, giving significant insight into knowledge for preservation and breeding initiatives. A study of genetic diversity could complement morpho-agronomic traits in future research to learn more about how genetic variation affects environmental adaptation.