Variety in video sampling protocol for coral reef survey worldwide has prompted this study to create an optimized protocol for Coral Video Transect (CVT) technique for coral reef survey in Malaysia. The effect of different vertical distance of the camera above the substrate during video recording, number of frames and points analyzed as well as time spent during field and analysis were examined to determine an optimal protocol for CVT technique at different coral reef conditions in Malaysia's water. Video recording taken at 0.5 m camera distance was selected as optimize vertical distance above the substrate as it can identify more benthic categories than 1.0 m with lesser time taken as well as frames extracted than 0.2 m. Respectively, 80% of total frames extracted from 20 m transect and analyzed with 50 points per frames were chosen as an optimized sample size for its ability to precisely estimate percent cover and accurately identify benthic categories. This optimized protocol was then compared with Line Intercept Transect (LIT) method. No clear difference in estimating percentage cover of major benthic categories between CVT and LIT method, but CVT recorded a significantly higher number of benthic categories with lesser time spent during field survey as compared to LIT method. This implied that the optimize CVT method can precisely estimate percent cover and accurately identify benthic categories in coral communities and are thus more suitable for scientific research and management purposes than LIT method. Other advantages of using this technique are by providing a permanent data that can be reassessed later on, lesser field time and wider survey area. Overall, this study showed that CVT technique is an acceptable alternative method of coral reef survey in Malaysia.