Background <p>The breeding process enables plants to inherit desirable traits, such as yield, flowering time, pest resistance, and cannabinoid and/or terpene content. As a result of these intensive genetic improvement practices, where genetically similar individuals or those from the same lineage are crossed, the expression of unfavorable recessive alleles may occur due to homozygosity. This can lead to less productive plants, increased susceptibility to diseases, and reduced quality. Despite the potential negative effects associated with inbreeding, self-pollination (a form of inbreeding) is a necessary cultivation technique used to obtain seeds that produce phenotypically female plants (feminized seeds) for commercialization and/or to fix desirable traits, albeit at the cost of reduced genetic variability. The Cannabis sativa L. seed market has grown significantly in recent decades, driven by the legalization and regulation of medicinal and recreational use. Self-pollinated feminized seeds are popular among growers and commercial seed banks because, in most cases, they guarantee that inflorescences will express the cannabinoid and terpene profile of the single parent plant.</p> <p>The objective of this work is to compare the morphological variation of seeds obtained from the reversal of female clones followed by self-pollination, and seeds obtained from crossing genetically distinct parental. To study seed shape and size, we employed 2D geometric morphometrics (GM) based on landmarks and semilandmarks, coupled with a supervised machine learning approach and multivariate statistical approach for analysis.</p> Results <p>No direct relationship was observed between size and seed type, although significant differences between varieties were detected. The shape of seeds from crosses between different parents (male and female) showed lower classification accuracy compared to feminized seeds. These results support the hypothesis that inbreeding reduces the variability, as feminized seeds from self-pollination were correctly identified at a high rate using a discriminant function.</p> Conclusions <p>Our research demonstrates that 2D geometric morphometrics can effectively distinguish and trace feminized and self-pollinated cannabis seeds. These seeds exhibit the least morphological variation, enabling accurate identification and providing a reliable foundation for practical applications. The Random Forest classifier's high performance confirms the effectiveness of using morphological traits for seed discrimination. These results open the door for advanced machine-learning techniques aimed to improve scalability and automation. </p>