Vocal individuality is essential for social discrimination but has been poorly studied in animals that produce communal signals (duets or choruses). Song overlapping and temporal coordination make the assessment of individuality in communal signals more complex. Additionally, selection may favor the accurate identification of pairs over individuals by receivers in year-round territorial species with duetting and long-term pair bonding. Here, we studied pair and individual vocal signatures in the polyphonal duets of rufous horneros Furnarius rufus, a Neotropical bird known for its long-term pair bonds. Hornero partners engage in duets to deter territorial intruders and protect their partnership year-round, and can discern duets from neighbors versus strangers. Using a dataset of 471 duets from 43 pairs in two populations, we measured fine-scale acoustic features across different duet levels (e.g., complete duets to non-overlapping syllable parts) and analysis levels (pair or individual). Permuted linear discriminant function analyses classified pairs and individuals more accurately than expected by chance (means: 45% and 47% versus 4 and 2%). Pair identity explained more variance in the multivariate acoustic features of duets than individual or population identities. The initial frequency of the duet showed strong potential for encoding pair identity. The acoustic traits contributing most to individual vocal signatures varied between sexes, which might facilitate the simultaneous assessment of duetters’ identities by receivers. Our study indicates that vocal individuality may exist even in species with intricate and innate communal signals and elucidates the mechanisms employed by horneros in their social discrimination ability.