In this study, we examine acoustic individuality in male duet songs of wild, non-habituated Bornean southern gibbons (Hylobates albibarbis) and identify contributing acoustic variables. We recorded 174 male duet songs from nine groups in a rainforest in Central Kalimantan, Indonesia. Each male portion of the duet was analysed for 14 acoustic variables at three levels of variation, including six note-specific variables (start frequency, end frequency, minimum frequency, maximum frequency, average frequency and duration), four phrase-specific variables (minimum frequency, maximum frequency, duration and number of syllables) and four song-specific variables (minimum frequency, maximum frequency, duration and number of syllables). Principal component analysis was performed to summarise each of these sets of variables into a total of six principal components (PCs). Strong acoustic individuality was found in all PCs and at all three levels: note, phrase and song (all p < 0.001). Furthermore, a particularly high magnitude of individuality was found in PC 1 of the song-specific analysis, defined by the acoustic variables of duration and number of syllables. Due to the high levels of individuality, we suggest that these acoustic variables may be used by Bornean southern gibbons for individual discrimination. As well as furthering our biological understanding of male gibbon song with regards to individuality and associated conspecific recognition, these findings also have the potential to help improve population survey methods, such as the acoustic sampling method using listening points, by offering a more accurate method of individual recognition.