Almond (Prunus amygdalus L.) is a major tree nut species and consumed worldwide. Morocco maintains a long-standing presence of domesticated almonds, hosting a secondary genetic diversity hotspot that demands safeguarding as an important resource for future almond breeding programs. Here, we assessed the pomological diversity of local Beldi almond ecotypes to detect elite trees based on nuts and kernels characteristics. A significant correlation was found among some studied variables. Principal Component Analysis (PCA) for quantitative traits showed that two components explained 78.91% of the total variation and revealed that traits related to fruits contribute to a large proportion of the observed variability. Then, a comprehensive genetic study of 98 almond accession including 93 of the Beldi ecotype and five non-Moroccan cultivars by analyzing 12 Simple Sequence Repeats markers showed high Polymorphism Information Content. We used population structure and PCA to analyze the molecular variance and described the genetic diversity of the identified subpopulations. We identified five subpopulations with little genetic differentiation, but two subpopulations have high genetic diversity. These subpopulations represent promising genetic pools developing novel almond cultivars that can provide high yield in adverse conditions, thereby fostering profitable Moroccan breeding programs for sustainable almond agriculture.