Genetic differentiation between the two karyotype forms I (2n = 60) and II (2n = 62), which have been recently recognized in the Egyptian N. ehrenbergi, was examined at 17 structural genetic loci and interrelationship was discussed. Of these 17 genetic loci, 10 (58.8%) loci were monomorphic with the same allele fixed in all individuals from both karyotype forms and only 7 (41.2%) loci were polymorphic with two different alleles. Levels of genetic variability between the two forms were relatively low and are comparatively either within the range or quite different from those of the same species occurring elsewhere. The means of expected (He) and observed (Ho) heterozygosity were 0.175 ± 0.503 and 0.124 ± 0.496, respectively, the mean percentage of polymorphic loci (P) was 29.42%, while the mean number of alleles per locus (A) was 1.30 ± 0.11. In addition, the mean levels of genetic identity (I) and genetic distance (D) were 0.932 and 0.070, respectively, indicating that the two forms were genetically highly similar. Thus, the present results are concordant with that obtained from the chromosomal, morphological and penial study and support the recent hypothesis of occurrence of new species in N. ehrenbergi. Divergence between the two species would have occurred during Pleistocene (ca 1.26 million years ago).