Rabbit breeding offers a promising avenue for enhancing food security, reducing undernutrition, and alleviating rural poverty in developing countries. While the native Egyptian Gabali rabbit (GAB) exhibits superior adaptation to arid environments, its growth rate is comparatively lower than that of exotic breeds such as the New Zealand White (NZW). Hybridization programs between GAB and NZW are therefore crucial for improving growth performance while retaining the Gabali’s desirable hardiness. This study investigated molecular genetic variation among four rabbit lines: GAB, NZW, and their reciprocal crosses, including F1 and backcross generations (n = 744 born, 621 weaned; derived from 14 sires and 50 dams). We used 18S rDNA gene sequencing to assess genetic diversity and differentiate purebreds from their hybrid offspring. Phylogenetic analysis of 18S rDNA sequences revealed distinct genetic relationships among the lines. Results demonstrated that NZW and F1 crosses (♀NZW×♂GAB) exhibited significantly higher body weights compared to the GAB breed (P < 0.01), which consistently displayed lower weights, indicative of slower growth. Notably, the ♀NZW×♂GAB cross exhibited the highest weight gains, highlighting the influence of genetic variation on growth performance (P < 0.01). This information is crucial for optimizing breeding strategies to maximize heterosis and ultimately enhance the productivity and profitability of rabbit farming.