As the urbanization has been increasing, many bird species have been selected out of urban environments. Nevertheless, a few species such as Savanna Nightjars (Caprimulgus affinis) have been found to survive successfully in urban areas of Taiwan. Although there have been many researches on acoustic adaptation to noise in urban oscines, little has been done on nocturnal non-passerines. The aim of this study is to investigate the vocal individuality of the Savanna Nightjar and acoustic parameters of their calls associated with different levels of noise in Taiwan. A total of 1925 calls were recorded from 67 individuals in 8 different areas. We found that 30 acoustic parameters demonstrated significant individual differences and 84.6% of calls could be correctly classified to 67 individuals based on those acoustic parameters. Fifteen acoustic parameters were found to be significantly related to noise levels (noise-related) and the other 15 parameters were not (noise-unrelated). The discriminant function using noise-unrelated parameters had a higher correct classification rate than that using noise-related parameters (75.9% vs. 51.8%). We therefore conclude that acoustic parameters related with noise levels might not be suitable for individual identification in Savanna Nightjars.