Recent studies have shown evidence of a significant decline of the Posidonia oceanica (P.O.) meadows on a global scale. The monitoring and mapping of these meadows are fundamental tools for measuring their status. We present an approach based on a deep neural network to automatically perform a high precision semantic segmentation of the P.O. meadows in sea-floor images, offering several improvements over the state-of-the-art techniques. Our network demonstrates outstanding performance over diverse test sets, reaching a precision of 96.57% and an accuracy of 96.81%, surpassing the reliability of labeling the images manually. Moreover, the network is implemented in an autonomous underwater vehicle, performing an online P.O. segmentation, which will be used to generate real-time semantic coverage maps.