Underwater video techniques are more frequently being used in marine ecology studies. A technique called Coral Video Transect (CVT) was used to quantify percentage cover of benthic organisms within Sembilan Island Archipelago and Jarak Island, Malaysia in determining the coral community structure of the West Coast of Peninsular Malaysia. The survey was conducted in shallow water reef with a mean depth of 10.4±1.4 m deep. A total of 22 identified coral genera from 11 families were identified. A higher number of coral genera were found within Sembilan Island Archipelago (20 coral genera) as compared to Jarak Island (11 coral genera). The entire reefs were in ‘poor’ condition with mean total percentage coral cover ranging from 2.63%-23.84%. The reefs were dominated by massive and encrusting coral with decreasing order of percentage cover as followed; Porites>Tubastrea>Diploastrea>Echinophyllia. The use of CVT technique to describe the reef status was recommended as it can provide a permanent record for subsequent studies and for future comparison later on. The data presented might be useful for resources sustainability or coral reef management in Malaysia.