Urbanization is known to cause noticeable changes in the properties of local climate. Studies have shown that urban areas, compared to rural areas with less artificial surfaces, register higher local temperatures as a result of Urban Heat Islands (UHIs). Hong Kong is one of the most densely populated cities in the world and a high proportion of its population residing in densely built high-rise buildings are experiencing some degrees of thermal discomfort. This study selected Mong Kok and Causeway Bay, two typical urban communities in Hong Kong, to gather evidence of microclimate variation and sources of thermal discomfort. UHIs were estimated from 58 logging sensors placed at strategic locations to take temperature and humidity measurements over 17 consecutive days each in the summer/hot and winter/cool periods. By employing geographic information and global positioning systems, these measurements were geocoded and plotted over the built landscape to convey microclimate variation. The empirical data were further aligned with distinct environmental settings to associate possible factors contributing to UHIs. This study established the existence and extent of microclimate variation of UHI within urban communities of different environmental configuration and functional uses. The findings provided essential groundwork for further studies of UHI effects to inform sources of local thermal discomfort and better planning design to safeguard environmental health in public areas.