Cannabis sativa stands out as an important crop with significant socioeconomic importance in the Rif Mountains of North Morocco. Recently the number of new cultivars developed in this region has gradually increased for different purposes. In this current study, we delve into the eco-anatomical characteristics of stems across six of the most prevalent Cannabis sativa cultivars in Morocco: ‘Avocat’, ‘Beldiya’, ‘Critical Plus’, ‘Industriel’, ‘Khardala’, and ‘Mexicana’. The investigation encompasses the measurement and analysis of six key eco-anatomical traits: plant height, stem diameter, vessel size, vessel density, number of vessels joined in radial files, and coefficient of hydraulic conductivity. Our aim is to elucidate the variations among these cultivars and underscore their agricultural and ecological relevance. Through anatomical examinations of stem cross-sections, our findings reveal notable disparities and distinctive features among the cultivars. The ‘Khardala’ cultivar exhibits the highest values across most measured eco-anatomical traits, while ‘Beldiya’ and ‘Mexicana’ show similar trait values, particularly with low stem diameter and vessel density. In contrast, ‘Industriel’ stands out with the lowest vessel size and highest vessel density. ‘Critical Plus’ and ‘Avocat’ closely resemble ‘Khardala’ in vessel size and stem diameter. Regarding hydraulic conductivity, ‘Khardala’ ranks highest, followed by ‘Avocat’ and ‘Critical Plus’, while ‘Industriel’ registers the lowest. Our findings underscore increased water demand and uptake potential in ‘Khardala’, ‘Critical Plus’, and ‘Avocat’, contrasting with ‘Industriel’, ‘Beldiya’, and ‘Mexicana’. Anatomical diversity among Cannabis cultivars in our study likely stems from genetic lineage and ecological adaptation.