A mitochondrial mutant strain of D. subobscura has two mitochondrial genome populations (heteroplasmy): the first (20-30% of the population, 15.9 kb) is the same as could be found in the wild type; the second (70-80% of the population, 11 kb) has lost by deletion several genes coding for complex I and III subunits, and four tRNAs. In human pathology, this kind of mutation has been correlated with severe diseases such as the Kearns-Sayre syndrome, but the mutant strain, does not seem to be affected by the mutation (1). Studies reported here show that: a) Transcripts from genes not concerned by the mutation are present at the same level in both strains. b) In contrast, transcript concentrations from genes involved in the deletion are significantly decreased (30-50%) in the mutant. c) Deleted DNA was expressed as shown by the detection of the fusion transcript. d) The mtDNA/nuc.DNA ratio is 1.5 times higher in the mutant strain than in the wild type. The mutation leads to change in the transcript level equilibrium. The apparent innocuousness of the mutation may suggest some post-transcriptional compensation mechanisms. This drosophila strain is an interesting model to study the consequence of this type of mitochondrial genome deletion.