This study investigates the potential threats or conflicts shadowing social harmony in Johor Malaysia. The State of Johor is inhabited by plural, yet, segregated ethnic groups, thus making them prone to communal conflicts. The process of data collection was conducted between 2010 and 2012 through interviews with 1,000 respondents from 10 regions as well as extensive field observations. The study shows that notwithstanding the conflict potential is confined to low-intensity and sporadic quarrel, the impact of tension which has frequently occurred within families and relatives can lead to clashes in a larger community. In turn, this incites various kinds of prejudice among the fragmented communities. Worse still, the individual perception about tolerance in respect to religious aspects is quite concerning, albeit not demonstrable in the context of inter-ethnic relations. Nonetheless, two most sensitive issues perpetrating social incompatibilities are detected as to the construction of worship places and defamation against different religious identities.