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The assessment of anthropogenic impacts on coastal waters is an important task to accomplish under the European Water Framework Directive (WFD 2000/60/EEC). Macroalgae are one of the biological quality elements that must be considered, but their assessment has been generally limited to intertidal areas due to the difficulties and costs associated with working in subtidal areas. In this work, the suitability of using landscape mosaicing techniques is analyzed for the application of the “Quality of Rocky Bottoms” index (CFR by its Spanish acronym) in subtidal areas. For this purpose, the sensitivity and accuracy of both the indicators that compose the CFR index (characteristic macroalgae coverage, fraction of opportunistics and characteristic macroalgae richness) and the index itself were tested against different sampling surfaces and validated through direct applications of the CFR carried out in situ by scuba divers. The study was carried out at three sites, located on the coast of Cantabria (N. Spain), covering a variety of environmental conditions (depth ranges and anthropogenic pressures). Underwater video transects of 5-20 m length were recorded by scuba divers and processed with specialized software to build continuous image mosaics of the assessment sites. Each mosaic was inserted into a Geographical Information System where all distinguishable macroalgae species were identified and their coverages were estimated. Replicated subsamples of different areas (0.25 m2, 0.5 m2, 1 m2 and 2.5 m2) were tested from each mosaic for the estimation of both the single indicators and the CFR index itself. Main results showed that larger subsample areas produced higher and more accurate CFR values, mainly related to higher richness values and to smaller variability within the replicates. Accordingly, the minimum sample size required to carry out this type of studies was estimated to be of 2.5 m2, showing no significant differences with the total mosaics. At this spatial scale, the assessments of the CFR index using mosaics showed a significant correlation and an excellent agreement with the results obtained in situ. In summary, underwater video mosaicing techniques proved to be a useful tool for the application of the CFR index and could also be of great interest for the study of subtidal environments by allowing visualization of extensive seafloor areas.