Dystroglycan (DG) is a widely expressed extracellular matrix (ECM) receptor required for muscle viability, synaptogenesis, basement-membrane formation and epithelial development. As an integral component of the Dystrophin-associated glycoprotein complex, DG plays a central role in linking the ECM and the cytoskeleton. Disruption of this linkage in skeletal muscle is the underlying cause in various types of muscular dystrophies (MD). One particular type of MD is caused by alterations of O-linked glycosylation in the mucin-like domain of DG, which is required for binding of the ECM molecules Laminin and Perlecan. In epithelial cells, reduced expression of DG is associated with increased invasiveness of cancer cells and loss of cell polarity. Drosophila Dg is, in contrast to vertebrate Dg, subjected to differential splicing of the mRNA. Interestingly, the shorter DG splice forms lack the mucin-like domain. Here, we describe the embryonic expression patterns of full-length DG and a short variant of DG. We find that differential splicing of Dg is developmentally regulated and tissue-specific. In some tissues, e.g., hindgut, midgut constrictions, gonads, both DG variants can be detected. For the long form, we detected specific expression at the blastoderm stage, in the epidermis and in the tracheal pits. The short form showed exclusive expression in dorsal vessel cells, chordotonal organs and dorsal median cells. In the nervous system, the long form is predominantly expressed on axons, while the short form is present on glial cells. Our findings further support the idea that DG forms lacking the mucin-like domain serve a specific function in Drosophila.