Paper as accepted for publication in TrAc Analytical techniques for discovery bioactive compounds from marine fungi Katia Duarte, Teresa A. P. Rocha-Santos, Ana C. Freitas, Armando C. Duarte Abstract Marine fungi are a promising source of novel bioactive compounds as lead structures for medicine and for plant protection. The current analytical techniques and future perspectives of analytical methodologies are reviewed from the point of view of the discovery and the characterization of bioactive compounds isolated from marine fungi. This critical overview also includes a general assessment of sampling and preparation of extracts, the comparison of different methods used for separation and isolation, as well as different strategies used for structural characterization of the bioactive compounds. The evolution of the application of the bioassays for discovery of bioactive compounds is also ascertained. Finally, this review addresses the advantages and disadvantages of such techniques, and comments on future applications and potential research interest within this field. Keywords: marine, fungi, analytical, extraction, separation, bioactivity Katia Duarte, Teresa A. P. Rocha-Santos*, Ana C. Freitas ISEIT/Viseu, Instituto Piaget, Estrada do Alto do Gaio, Galifonge, 3515-776 Lordosa, Viseu, Portugal Teresa A. P. Rocha-Santos*, Ana C. Freitas, Armando C. Duarte CESAM (Centre for Environmental and Marine Studies) & Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal Corresponding author: E-mail: teralex@viseu.ipiaget.org; ter.alex@ua.pt 1. Introduction Oceans cover more than 70% of the world´s surface and have a wide diversity of marine organisms such as fungus which offer a rich source of natural compounds with biological activity (bioactive compounds) [1, 2]. Mayer et al. [3] used a modification of Schmitz’s chemical classification to assign marine natural product structures to six major chemical classes: polyketides, terpenes, peptides, alkaloids, shikimates, and sugars (Table 1). Marine fungi have been widely studied [4-6] for their bioactive metabolites and these organisms have proven to be a rich and promising source of novel