Vernacular architecture is architecture built using commonly found materials found within the surrounding area of the native community. Vernacular architecture in Asian countries include heritage buildings such as timber houses and they are the most common type of traditional buildings found throughout the East and South-East Asia. The importance of the usage of locally sourced materials such as timber, bamboo, and even stones contributed to the unique designs of traditional dwellings found in different cultures throughout the world. Due to this, there are many architectural design similarities in vernacular buildings such as those found in Japan and Malaysia. This study focuses on traditional townhouses in Kyoto, Japan, known as Kyomachiya and the traditional townhouses in Malacca, Malaysia. Traditional Kyomachiya are heritage buildings related to the vernacular architecture of Japan that functions as both residential buildings and commercial buildings. Traditional Kyomachiya are timber townhouses with multiple functions, and they are similar to that of traditional townhouses in Malacca, Malaysia in terms of building materials, functions and typologies. This study aims to investigate and compare the architecture of Kyomachiya in Japan to that of traditional townhouses in Malacca, Malaysia. The objectives of this research are firstly, to investigate the design layout of Machiya and Malacca shophouses, and secondly, to compare the functionalities of the townhouses which, information gathered can be used for future conservation works. The methodologies of this study are case studies of Kyomachiya and Malacca townhouses, document and content analysis through archival research, and on-site observations. The findings indicated the similarities and differences in the architecture of the heritage buildings through their layouts, design elements, functions for the importance of preserving and conserving the Kyo-Machiya in Japan and the townhouses in Malaysia for future generations to come.