Structural polytene chromosome maps of the two Tephritid (Order- Diptera) fruit fly species were studied. Bactrocera zonata originates in South and South-East Asia. It attacks more than 50 host plants, several of which are commercial species- guava, mango, peach, apricot, fig and citrus. The probable risk of its introduction to a new country is aided by travel and trade, and is influenced by changes in climate and land use. The EPPO classified it as A1 Pests, suggesting for regulation as a quarantine pest. Zeugodacus tau is widespread in Asia and Australia. It attacks 34 hosts from 9 families, major commercial hosts- melon, cucumber, pumpkin, luffa, sapodilla, bitter gourd and guava. The aim of the study was to identify polytene chromosomes from the 3^rd instar larval salivary glands and to construct structural polytene maps based on the banding patterns of the polytene arms. In both species, five polytene chromosomes (10 polytene arms) corresponding to the five autosomes of the mitotic chromosomes and a heterochromatic mass were observed in polytene nuclei. Heterochromatic mass is a granular network and supposed that it corresponds to sex chromosomes. Polytene maps were constructed by dividing each of chromosome arms into twenty sections. The tips of each chromosome arm, prominent landmarks, characteristic banding patterns and puffs were recognized that reflected the fundamental differences in the chromosomes. The structural map presented here could help to explain each section of the chromosome arm which allow to identify/ locate any chromosomal rearrangements or any structural differences within other tephritid species.