The development of a population-specific reference genome is crucial for increasing the accuracy of genomic analyses and advancing precision medicine. This study explores the use of recurrent genetic variants as an alternative approach to construct a full reference genome for the Moroccan population. We analyzed genomic data from 32 female Moroccan participants, identifying a total of 3,902 variants, with a notable concentration of variants on chromosome 13 compared with chromosome 17. Among these, 24 variants were found in more than 25% of the samples, and 5 were found in more than 50% of the samples. The majority of identified variants were missense, with some synonymous and intron variants. Our findings indicate that focusing on recurrent variants provides a cost-effective and practical method for representing the genetic diversity of the Moroccan population. This approach minimizes ethnic bias and enhances the relevance of genetic markers for health research. Although many variants are categorized as benign or of unknown significance, they serve as valuable markers for understanding population-specific genetic characteristics. This study lays the groundwork for future research and the development of a population-specific reference genome, ultimately contributing to more precise and culturally relevant genomic analyses in Morocco.