Changes in the salivary gland chromosomes are described in sibling species Prodiamesa olivacea Mg. and P. bureshi Michailova larvae collected from trace metal polluted and unpolluted areas in Bulgaria and the United Kingdom. Although both species from polluted and unpolluted areas show a high frequency of ectopic conjugations, those between arm B (telomere) and arm F occur at a significantly higher frequency in P. bureshi from unpolluted sites. The reasons for chromosome conjugations and their changes under stress conditions are discussed. Regression of the puff in section 2 of chromosome arm A was significantly higher in P. bureshi from polluted sites, suggesting that trace metal pollution represses transcription at that site. Also, somatic heterozygous inversions and deficiencies occur in chromosomes of both species at the polluted areas. Some deformities of the head capsule were observed in both species at the metal-polluted sites. However, our data shows that the genome is a much more sensitive indicator of trace metal pollution than external morphology. The present authors suggest that measuring genotoxic damage at a cellular level provides a subtle and cost-effective indicator of trace metal pollution.