While the issue of individual variation has been widely studied in second language learning or processing, it is less well understood how perceptual and musical aptitude differences can explain individual variation in native speech processing. In the current study, we make use of tone merger in Hong Kong Cantonese, an ongoing sound change that concerns the merging of tones in perception, production or both in a portion of native speakers, to examine the possible relationship between tone merger and musical and pitch abilities. Although a previous study has reported the occurrence of tone merger independently of musical training, it has not been investigated before whether tone-merging individuals, especially those merging tones in perception, would have inferior musical perception and fine-grained pitch sensitivities, given the close relationship of speech and music. To this end, we tested three groups of tone-merging individuals with various tone perception and production profiles on musical perception and pitch threshold tasks, in comparison to a group of Cantonese speakers with congenital amusia, and another group of controls without tone merger or amusia. Additionally, the amusics were compared with tone-merging individuals on the details of their tone discrimination and production profiles. The results showed a clear dissociation of tone merger and amusia, with the tone-merging individuals exhibiting intact musical and pitch abilities; on the other hand, the amusics demonstrated widespread difficulties in tone discrimination yet intact tone production, in contrast to the highly selective confusion of a specific tone pair in production or discrimination in tone-merging individuals. These findings provide the first evidence that tone merger and amusia are distinct from each other, and further suggest that the cause of tone merger may lie elsewhere rather than being driven by musical or pitch deficits. We also discussed issues arising from the current findings regarding the neural mechanisms of tone merger and amusia.