Carob ( L. Fabaceae) is a species of significant economic, ecological, and cultural importance in the Mediterranean region. It is valued for its adaptability to various environments and wide-ranging agricultural and industrial applications. Despite its potential, the genetic characterization of this species in Algerian territories has received little attention to date. The present study aims to decipher carob's genetic structure and diversity in Algeria. This study presents a comprehensive morphological characterization of 39 Algerian carob accessions based on pod traits and molecular genotyping using eight nuclear and three chloroplast SSR markers across different geographical locations and environmental conditions. The morphological analysis revealed a discrete differentiation among accessions, primarily influenced by their area of origin. The genetic analysis identified 38 unique genotypes. Allelic richness indicated high polymorphism, with an average of 3.81 alleles and 5.36 genotypes for nuclear SSR markers. Chloroplast SSR markers showed lower variability but provided insights into population structure. Genetic analysis revealed distinct genetic clusters aligned with geographical and bioclimatic regions, supported by minimum spanning network analysis that showed the genetic flow patterns among accessions. Discriminant analysis of principal components identified five optimal sub-population groups, highlighting a genetic structure linked with different bioclimatic conditions. These findings evidence the complex genetic diversity of Algerian carob germplasm and offer valuable insights for the sustainable exploitation of carob genetic resources.