The Orang Asli, who are considered minorities in Malaysia, is divided into three groups – the Negrito, Senoi and Proto-Malays. Each group has its language used during oral communication. The Duano language is one of the indigenous languages under the Proto-Malay group. The language is classified under the Austronesian family of languages, similar to the Malay language. The Duano language is the language of the indigenous people who dwell in the state of Johor. Based on the scale presented by EGIDS in “Ethnologue” (2021), the Duano language is at risk of becoming moribund. Researchers also found that deep comparative studies of the phonological systems to be limited. Hence, this paper aims to examine the process of phonological changes in the Duano language by comparing it with the Standard Malay Language (BMS). This study utilises the upstream fieldwork approach, supported by conducting interviews, observations, recordings and note-taking. The structural theory was applied during analysis, whereby the Duano and BMS cognates were transcribed phonemically and classified under specific sub-systems. They were then analysed using a qualitative comparative perspective to examine the phonological differences that had occurred. Results showed that the Duano language had undergone phonological changes, such as phoneme alignment, glottalisation, monophthongisation and delineation. In conclusion, the phonological changes indicated an independent evolutionary process for both languages in a particular environment, eventually forming a distinct phonological innovation.