The acquisition of an acoustic template is a fundamental component of vocal imitation learning, which is used to refine innate vocalizations and develop a species-specific song. In the absence of a model, birds fail to develop species typical songs. In zebra finches (Taeniopygia guttata), tutored birds produce songs with a stereotyped sequence of distinct acoustic elements, or notes, which form the song motif. Songs of untutored individuals feature atypical acoustic and temporal structure. Here we studied songs and associated respiratory patterns of tutored and untutored male zebra finches to investigate whether similar acoustic notes influence the sequence of song elements. A subgroup of animals developed songs with multiple acoustically similar notes that are produced with alike respiratory motor gestures. These birds also showed increased syntactic variability in their adult motif. Sequence variability tended to occur near song elements which showed high similarity in acoustic structure and underlying respiratory motor gestures. The duration and depth of the inspirations preceding the syllables where syntactic variation occurred did not allow prediction of the following sequence of notes, suggesting that the varying duration and air requirement of the following expiratory pulse is not predictively encoded in the motor program. This study provides a novel method for calculation of motor/acoustic similarity, and the results of this study suggest that the note is a fundamental acoustic unit in the organization of the motif and could play a role in the neural code for song syntax.