Johor Strait has received massive anthropogenic traffic in recent years, causing environmental alteration and inevitably harming macrobenthos on the seafloor. A comprehensive assessment was done in several key locations within the strait to identify macrobenthic inhabitants and possible driving factors attributing to differences in macrobenthic assemblages in these areas. Sediments were acquired using Ponar Grab in 13 key locations within the Johor Straits. Seven hundred thirty macrobenthic individuals and 46 known taxa were identified in sediments of 13 locations in the strait. Annelids Prionospio (n=295), Minuspio (n=95) and Mediomastus (n=82) were concentrated in the central zone. Molluscs dominated the Merambong Shoals area (Arcualuta, n=66), and amphipods dominated waters off Santi River (Leucothoe, n=26; Gammarus, n=11; Cymadusa, n=9). PERMANOVA analyses (p<0.05) showed significant differences in benthic taxa composition in all locations overall. BIOENV analyses (r=0.76, p<0.05) highlighted water acidity, chlorophyll-a, silts and total organic carbon as the main influences toward benthic assemblages throughout the study area. PCA graph indicated higher organic carbon and silts in the central area, implying favourable conditions for Sedentarian polychaetes to thrive. The east and west ends of the strait exhibited higher readings of water acidity and chlorophyll-a, which may directly contribute to a higher diversity of benthic communities in the areas. Lower oxygen levels in two locations in the central area (J3=2.97 mg/L, J4: 2.63 mg/L) exhibited Sedentaria polychaete-dominated region, but zero benthic organisms in another part of the central area (J5-J9, 2.97–0.99 mg/L). This study showcased the effectiveness of environmental monitoring using macrobenthos as an indicating subject.