This study investigates the prosodic realization of negation in Saisiyat, an endangered aboriginal Austronesian language of Taiwan, and compares the prosodic properties of its affirmative and negative sentences with those of British English. In order to test Yaeger-Dror's "Cognitive Prominence Principle," according to which cognitively prominent items (such as negators) should be prosodically marked, we measure the F0 peak, the intensity peak, and duration of lexical items appearing in affirmative and negative sentences. Our results indicate that sentential subjects are the most acoustically prominent items with respect to F0 height and intensity in Saisiyat negative sentences, whereas the negator itself is the most acoustically prominent item with respect to F0 in an English sentence. In addition, the presence of a negator does not significantly change the prosodic parameters of contiguous words in Saisiyat. English, in contrast, exhibits relatively large-scale prosodic differences in both F0 and intensity between affirmative and negative sentences. This paper suggests that the following typological features can account for the differences observed between Saisiyat and English: (1) the relationship between prosodic prominence and syntactic subjects in Saisiyat, (2) transparency of the negation system in Saisiyat, and (3) the relationship between prosodic prominence and semantically defined focus in English.