Sphingolipids are important components of eukaryotic cell membranes. Some sphingolipid metabolites, such as ceramide, sphingosine and sphingosine-1-phosphate, also act as signaling molecules to mediate various biological processes, like programmed cell death. However, little is known about the mechanisms responsible for the abnormality in testis development in ceramidase knock down strain. Genomic information for the phenotype is currently unavailable, therefore, to facilitate research on it, we present a method for de novo assembly of drosophila transcriptome using short read sequencing technology (Illumina) combined with a tag-based digital gene expression (DGE) system. Illumina sequencing generated the drosophila transcriptome from the reproductive organ of two phenotypes with normal and abnormal testes. In total, we obtained 46,498,038 uniquely mapped reads that covered 87.53% of the current annotated transcripts, which represented 16246 mRNA transcripts, across all the samples. Among them, 34 differentially expressed genes (p < 0.05, false discovery rate q < 0.05) between the normal and abnormal testes were revealed, and we confirmed their altered expression levels by quantitative real-time PCR (qRT-PCR). Gene ontology and KEGG pathway analysis demonstrated that the 34 differently expressed genes were enriched in specific biological processes with regard to actin filament-based process, oxidative phosphorylation, metabolic pathways, phenylalanine metabolism and ECM-receptor interaction (p < 0.05). The obtained transcriptome and DGE profiling data provided comprehensive gene expression information at the transcriptional level that could facilitate our understanding of the molecular mechanisms of the abnormal testis development.