Using ultra-thin section electron microscopy, the development of the myotendon junction (MTJ) of Drosophila indirect flight muscle (IFM) is described for the first time. The MTJ is a cell-cell junction between the IFM and epithelial tendon cells. The terminal Z-band of each myofibril forms a uniform junction with a tendon cell; each junction shows a precise sequence of folding and elaboration in which microtubule arrays in both cell types play a prominent role. Upon IFM/tendon cell contact (by approximately 32 hr pupation), numerous flat, focal dense plaques form between muscle and tendon cell membranes. In the muscle, transient arrays of microtubules, which will form "sleeves" around the developing myofibrils, delineate the perimeter of these focal plaques. Each of the dense plaques enlarges and develops into the modified terminal Z-band (MT-Z) of a myofibril, linking the thick and thin filaments of the highly ordered terminal sarcomere to the membrane via a dense feltwork. As these plaques develop into the MT-Z, the perimeter of each plaque advances, leaving the central region deeply indented. Between 50-75 hr pupation, secondary folds appear in each MTJ, and tendon cell microtubules that will form the tendon elements attach to specific dense sites on the secondary folds of the junctional membrane opposite the MT-Z. By 100 hr pupation, each MTJ develops numerous sharp folds, thereby tightly interdigitating the muscle and tendon cell. Amorphous density associated with the junctional membranes assumes a crystalline array that includes the membrane cytoskeletons of both cells and the extracellular matrix. At the end of pupation (approximately 112 hr), the final link between tendon cell and cuticle is formed as the tiny, dense-tipped microvilli in contact with the cuticle are replaced by extracellular tonofibrils, dense shafts that fill deep pits in the tendon cell and extend deeply into the cuticle. The tendon cell microtubules become bundled and decorated by fine "feather" filaments and the free ends of these microtubule bundles become linked to the membrane surrounding the pits.