Seagrass meadows are considered to be the most important marine ecosystems for biodiversity, ecological, sedimentary and economic reasons. Their progressive degradation may be due to anthropogenic or natural disturbances, although losses of the seagrass meadows are mainly related to coastal development, pollution, trawling, fish farming, moorings, dredging, dumping and the competition with introduced species. As a consequence it is necessary to establish monitoring programs that follow a unified and complete protocol of actions to preserve these important marine resources. In this work we explore a procedure for monitoring the Posidonia oceanica and Cymodocea nodosa meadows by using image analysis through underwater photocamera, or alternatively, georeferenced towed underwater video-camera or remotely operated vehicles (ROV), in order to control the effects of submarine pipelines. The considered variables were: area, continuity, proximity, coverage percentage (using the software estimate), and species composition. The combination of these five variables were used to calculate the habitat structure index, H’. This method has several advantages over other techniques: 1) provides a permanent archive of visual images; 2) allows more objective estimates of changes over time; 3) give details of the meadows which is not possible with acoustics techniques;.4) allows to easily work over wide areas.