The blind mole rat Nannospalax ehrenbergi is considered a superspecies most likely containing many separate biological species. The most important reason for its taxonomic uncertainties is the remarkable morphological and chromosomal variation recorded within and between populations and species. This study presents a description and an analysis of a chromosomal, morphological (external and craniodental), and penial variation of N. ehrenbergi from El-Hammam, Matruh, Egypt. The results confirmed the occurrence of two karyotype forms (I and II) with different 2n, NF, and NFa number. Karyotype form I consists of 2n = 60, NF = 73, and NFa = 70, while karyotype form II, which is newly described here in Egypt for the first time, composes of 2n = 62, NF = 77, NFa = 74. This chromosomal variation between individuals of the two forms was accompanied by obvious differences in morphological measurements, presence or absence of supracondyloid foramen, position of hard palate in relation to the line connecting the rear edges of the alveoli of M3, position of the nasal posterior margin relative to the line connecting the upper or lower margins of the infraorbital foramen, and number of roots of M2 and M3. Although individuals of the two karyotype forms were similar in penial structural characteristics, they showed clear differences in the general shape of glans penis and size of baculum. The baculum was segmented and consists of a thick basal segment or proximal baculum that starts with a broad base and a thin terminal segment or distal baculum that ends with blunt tip. Accordingly, we could suggest that an evolutionary process has likely occurred in the Egyptian N. ehrenbergi and led to the formation of a new putative species with different chromosomal, morphological, and penial characteristics.