Alternative splicing can greatly increase the transcriptome and proteome complexity of an organism. It can also be an important mechanism for sexual dimorphism, as it allows males and females to express different proteins. While differential gene expression and genome location have been vastly studied to explain sexual dimorphism in both Drosophila and mammals, the extent to which different splice forms are found in male and female tissues, and their direct contribution to sexual differentiation, are still not fully understood. Previous work in Drosophila has looked at this question using only short RNA-seq reads, which makes it difficult to call different splice forms, as it requires an assembly step that may fail to discriminate between similar isoforms. Here, we use long read sequencing to not only identify spliceforms that are sex-specific but also to quantify the frequency of known sex-specific spliceforms in D. melanogaster, such as those for genes transformer, fruitless and sex-lethal. We sequenced male and female heads, mid-guts, and gonads using PACBio SMRT long-read sequencing to fully analyse exon usage and detect unique transcripts in different organs and sexes. Our study provides a more detailed characterization of alternative splicing in these tissues of D. melanogaster than was previously available, and allows us to carefully assess the extent to which splicing differs between sexes of this model organism, an important step towards understanding the role of alternative splicing in sexual differentiation. Our pipeline allows for the identification of splice forms that are unique to each sex and tissue as well as check for the diversity found in them.