The whiteleg shrimp Penaeus vannamei is one of the most relevant aquaculture species in Latin America and globally. Among several elements, the improvement of its production depends on the larval genetic quality produced in commercial hatcheries. A strategy for achievement is setting up a long-term management plan that includes the genetic settlement of a breeding population with broad genetic variability and reduced inbreeding levels and the design of adequate management and crossbreeding schemes. The settlement of the breeding population requires a detailed characterization of the genetic composition and diversity of the breeding line(s) that are being managed. The present study evaluated the genetic composition of six wild populations from the southern and northern coasts of the Mexican Pacific (Oaxaca, Guerrero, Nayarit, and Sinaloa) and 56 breeding lots maintained in commercial hatcheries. The genetic profiles of a low-density SNP marker panel (171 and 152 loci for the wild and hatchery-reared groups, respectively) were used to estimate genetic diversity and differentiation within and among samples. The wild population presented significant genetic differences between southern and northern Pacific locations. Although these populations showed higher diversity levels than the cultivated stocks, the genetic pool of the total 56 lots was highly variable with low inbreeding levels. The genetic characteristics of the analyzed populations and cultivated stocks warrant the constitution of a Mexican-origin breeding line with future potential for selection to the environmental conditions of the northwestern region of Mexico.