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The article discusses research which aims to analyze fungal occurrence, genetic diversity, and similarity between marine fungi gathered from Cascais and Sesimbra marinas located in Portugal. Details about the experimental design of the Fagus sylvatica and Pinus pinaster baits submerged in the marinas which include dimension and depth of submersion are presented. Following culture selection, DNA extraction, polymerase chain reaction (PCR) amplification, and genetic sequencing were performed. The frequent and very frequent marine fungi observed are also reported.