Telomeres are repetitive sequences of non-coding DNA found at the ends of eukaryotic chromosomes. Here, telomere banding patterns were detected in the salivary gland polytene chromosomes of Bactrocera zonata and Zeugodacus tau by C-banding technique. Both species infest a wide number of fruits and vegetables in tropical, sub-tropical and temperate regions of the world. Studies of polytene genomes of these and other tephritid fruit flies have been of great value in elucidating aspects of chromosome structure, gene activity and serving as tools for identification that can be critical for adoption novel control strategies to control these pests. Polytene genome of these species consists of five (2-6) banded chromosomes with ten polytene arms. Long arms are abbreviated as Left (L) and short arms as Right (R). In B. zonata, 2L telomere is slightly swollen with a combination of heterochromatic and euchromatic parts, 2R is totally heterochromatic. 3L tip has dotted heterochromatic cover, while 3R tip is rounded heterochromatic. 4L and 4R telomeres are rectangular with dense heterochromatic accumulation in ending caps. 5L telomere is expanded with dotted heterochromatic, 5R is rounded with heavily heterochromatic cap. 6L telomere is rhomboid and heterochromatic, while 6R is rounded and euchromatic. In Z. tau, 2L telomere is convex and euchromatic, 2R is straight and heterochromatic. 3L telomere is densely heterochromatic, 3R is comparatively flattened with dotted heterochromatic material. 4L and 4R tips are straight and highly heterochromatic. 5L and 5R have extensive euchromatic telomeres, but 5L end is heterochromatic, 5R is euchromatic. 6L is expanded and largely heterochromatic, whereas 6R telomere largely euchromatic. In fruit flies, telomeres of polytene chromosomes may serve as a cover for chromosome tips to protect them from nucleolytic degradation, recombination, repair and interchromosomal fusion. Thus, they play a vital role in maintaining chromosomal stability and preserving information in the genome.