The present Guide was prepared in the framework of the ECOMARE project, a concerted action of the European Community Marine Science and Technology Programme (MAST III) concerned with the ecological effects of Marine Protected Areas (MPAs) in the Mediterranean. The overall aim of ECOMARE was to unite and coordinate the efforts of a broad group of research teams involved in assessing the effects of protection (cessation of fishing) in Mediterranean littoral ecosystems. The specific objectives of this project were:- To establish the state of knowledge of the responses of marine communities to protective measures in Mediterranean littoral ecosystems;- To identify the main research needs and steps forward to progress from the assessment of effects on exploited populations to the assessment of effects at the ecosystem level;- To review and recommend working methodologies so that future investigations could be carried out in a coordinated and comparable manner.The second objective lead to the identification of three priority areas for future research in Mediterranean marine reserves: assessing biomass export from MPAs, assessing impacts of human activities in MPAs, and studying indirect effects of protection (e.g., fishurchin- algae interactions). The third objective lead to the preparation of the present guide on recommended methods for future research, with chapters addressing each of these priorities.The aim of this guide is not to describe each method in depth, but rather to present them briefly, with their advantages and limitations, and to provide references for further reading.