The steroid hormone ecdysone triggers transitions between developmental stages in Drosophila by acting through a heterodimer consisting of the EcR and USP nuclear receptors. The EcR gene encodes three protein isoforms (EcR-A, EcR-B1, and EcR-B2) that have unique amino termini but that contain a common carboxy-terminal region including DNA-binding and ligand-binding domains. EcR-A and EcR-B1 are expressed in a spatially complementary pattern at the onset of metamorphosis, suggesting that specific responses to ecdysone involve distinct EcR isoforms. Here, we describe phenotypes of EcR-A specific deletion mutants isolated using transposon mutagenesis. Western blot analysis shows that each of these mutants completely lacks EcR-A protein, while the EcR-B1 protein is still present. The EcR(112) strain has a deletion of EcR-A specific non-coding and regulatory sequences but retains the coding exons, while the EcR(139) strain has a deletion of EcR-A specific protein coding exons but retains the regulatory region. In these mutants, the developmental progression of most internal tissues that normally express EcR-B1 is unaffected by the lack of EcR-A. Surprisingly, however, we found that one larval tissue, the salivary gland, fails to degenerate even though EcR-B1 is the predominant isoform. This result may indicate that the low levels of EcR-A in this tissue are in fact required. We identified yet another type of mutation, the EcR(94) deletion, that removes the EcR-A specific protein coding exons as well as the introns between the EcR-A and EcR-B transcription start sites. This deletion places the EcR-A regulatory region adjacent to the EcR-B transcription start site. While EcR(112) and EcR(139) mutant animals die during mid and late pupal development, respectively, EcR(94) mutants arrest prior to pupariation. EcR-A mutant phenotypes and lethal phases differ from those of EcR-B mutants, suggesting that the EcR isoforms have distinct developmental functions.