In recent years, the gasotransmitter hydrogen sulphide (H
2
S), produced by the transsulphuration pathway, has been recognized as a biological mediator playing an important role under normal conditions and in various pathologies in both eukaryotes and prokaryotes. The transsulphuration pathway (TSP) includes the conversion of homocysteine to cysteine following the breakdown of methionine. In
Drosophila melanogaster
and other eukaryotes, H
2
S is produced by cystathionine β-synthase (CBS), cystathionine γ-lyase (CSE), and 3-mercaptopyruvate sulphurtransferase (MST). In the experiments performed in this study, we were able to explore the CRISPR/Cas9 technique to obtain single and double deletions in homozygotes of these three major genes responsible for H
2
S production in
Drosophila melanogaster
. In most cases, the deletion of one studied gene does not result in the compensatory induction of two other genes responsible for H
2
S production. Transcriptomic studies demonstrated that the deletions of the above
CBS
and
CSE
genes alter genome expression to different degrees, with a more pronounced effect being exerted by deletion of the
CBS
gene. Furthermore, the double deletion of both
CBS
and
CSE
resulted in a cumulative effect on transcription in the resulting strains. Overall, we found that the obtained deletions affect numerous genes involved in various biological pathways. Specifically, genes involved in the oxidative reduction process, stress-response genes, housekeeping genes, and genes participating in olfactory and reproduction are among the most strongly affected. Furthermore, characteristic differences in the response to the deletions of the studied genes are apparently organ-specific and have clear-cut sex-specific characteristics. Single and double deletions of the three genes responsible for the production of H
2
S helped to elucidate new aspects of the biological significance of this vital physiological mediator.