Mutually exclusive splicing is an important mechanism in a wide range of eukaryotic branches to expand proteome diversity, but the extent of its distribution within a single species and its evolutionary conservation is unknown. Here we present a genome-wide analysis of mutually exclusive spliced exons (MXEs) in Drosophila melanogaster at unprecedented depth. Most of the new MXE candidates are supported by evolutionary conservation, transcriptome data analysis and identification of competing RNA secondary structural elements. The enrichment of the genes with MXEs in transmembrane transporters and ion channel activity is consistent with findings in humans, although the MXEs appeared independently and in non-homologous genes, supporting the idea of a universal benefit of adapting ion channel and receptor properties by tandem exon duplications. The comparison of the mutually exclusive spliced exomes within the Drosophila clade shows high numbers of MXE gain and loss events, suggesting a role of these processes in speciation.