BACKGROUND: The effects of small-scale disturbances, such as monsoon, are understudied in tropical regions. The storms associated with monsoon events not only modify the local macroalgal community structure, but also reveal the continuation of short-term recolonisation. Thus, this study aims to determine the variation in species, assemblage and cover of macroalgae during the monsoonal cycle from 2015 to 2016. This paper presents data on the spatial and temporal distribution of benthic macroalgae along the coastline of Johor, Malaysia. The information is presented as raw and partially-processed data, which summarises the cover and frequency of macroalgae at the respective study sites. This paper describes an important set of data that can be used further for in-situ experiments on the effects of environmental disturbances towards pioneer and climax species in tropical areas.NEW INFORMATION: This study provides a description of the east coast shore of Peninsular Malaysia, specifically in Johor coast in 2015-2016. The spatial and temporal distribution and abundance of a total of 41 taxa were assessed at four monsoon-exposed locations. These data provide a comprehensive baseline against disturbance and recolonisation of macroalgal community can be effectively and objectively evaluated.