Hybridization modifies the genetic structure of the individuals or populations and affects the phenotypic stability depending on the genetic diversity of closely related species. In some cases, it exposes strong heterotic characters or disrupts their developmental stabilities due to new interrogated and/or broken gene(s). To check these inferences, we crossed Bactrocera zonata ♂ and B. dorsalis ♀ at a 1:3 ratio and studied their mitotic metaphase chromosomes following air drying and C-banding techniques at the CBR lab, IFRB, AERE, Dhaka. We examined five pairs of autosomes and one pair of sex chromosomes (parents and the hybrid). Karyotype morphology and heterochromatin distribution in mitotic metaphase chromosomes of B. zonata were studied and have already been reported. The total chromosome length of B. dorsalis and the hybrid was 47.16 µm and 33.18 µm, respectively. Chromosome 2 was the longest and the sex chromosome (X) was smallest except in the hybrid where 6 was the smallest one. Chromosomes 4 and X were metacentric, and 5 and 6 were submetacentric in all cases. Chromosome 2 was metacentric and Chromosome 3 was submetacentric in B. dorsalis and the hybrid. The Y chromosome was dot-shaped and fully heterochromatic. The B. dorsalis female contained more heterochromatin block than its male while the opposite scenario was found in the hybrid. Chromosomes 2, 3 and 4 had pericentric and 5, 6 and X had centromeric heterochromatin block. The hybrid was composed of the largest telomeric band in the X chromosome long arm. Due to genetic introgression, the hybrid's resulting autosome's length of was similar to that of its parental father (B. zonata) and its morphology was similar to that of its parental mother (B. dorsalis). Genetic material transmission from B. zonata to B. dorsalis or vice versa was a positive sign that B. zonata would become a new member of the B. dorsalis species complex that mediates in active pest management program.