Benthic communities are dynamic systems that are changing due to natural or anthropogenic impacts. For the purpose of an effective management of protected and endangered marine areas it is necessary to develop a permanent monitoring program for the benthic communities. One of the methods that can be used to monitor benthic communities, in particular Posidonia oceanica meadows, is a submarine geo-referenced videography. The aim of this study was to record the state of benthic habitats in shallow infralittoral of the National Park Kornati, using the original method of underwater geo-referenced videography as well as to determine the type and relative density of vegetation cover in the studied area. During the fieldwork we recorded 52 geo-positioned video-transects, with the total length of 28.4 km, of which Posidonia covered 14.8 km. Research has shown that the highest density of Posidonia meadows were at about 12 m of depth, with increased depth (decreased light intensity) density was reduced. Density of algal cover also decreased with depth, while the settlements of sparse Cymodocea and loose algae occurred at lower depths than those where the algae or Posidonia dominated. The highest density of algae and sparse Cymodocea settlements were at about 9 m of depth. The pen shell (Pinna nobilis) most often appeared at about 11 m of depth. The results confirmed that the underwater geo-referenced videography can provide high-quality data (spatial and visual), that they can be quickly collected, that they can be quantitatively analyzed, and that the method does not damage the benthic habitats and organisms. Since the data are georeferenced it is possible to return to the exact location after a certain time and re-record the same transect. The quantitative analysis of two data sets provides the exact insight into the state of habitat. Therefore, this method is very suitable for monitoring of benthic habitats.