Almond (Prunus dulcis Miller [D. A. Webb] or 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. However, detailed information on genetic diversity is lacking, particularly for the traditional (Beldi) almonds propagated for centuries from seeds, representing the original cultivar pool. Here, we assessed the pomological diversity of local Beldi almond ecotypes to detect elite trees based on nuts and kernels characteristics. A high degree of variability was obtained. 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 (SSRs) markers with high Polymorphism Information Content (PIC). We used population structure and Principal Coordinates Analyses (PCoA) to analyze the molecular variance and described the genetic diversity of the identified subpopulations. We identified five subpopulations with little genetic differentiation between the populations, but two subpopulations have high genetic diversity. These subpopulations represent promising genetic pools that necessitate full protection. They are a significant resource for developing novel almond varieties that offer high yields in adverse conditions, fostering profitable Moroccan breeding programs for sustainable almond agriculture.