the objective of this work was to isolate and characterize filamentous fungi present in different stages of harvest, fermentation, drying and storage of coffee beans processed by natural method. the cherries were hand-picked and then placed on a cement drying platform where they remained until reached 11% of humidity. microbial counts were found in all samples during fermentation and drying of the coffee beans. counts of fungi in the coffee cherries collected from the tree (time 0) were around 1.5 x 103 cfu/g. this number increased slowly during the fermentation and drying reaching values of 2 x 105 cfu/g within 22 days of processing. two hundred and sixty three isolates of filamentous fungi were identified. the distribution of species during fermentation and drying was very varied while there was a predominance of aspergillus species during storage period. the genera found were pestalotia (4), paecelomyces (4), cladosporium (26), fusarium (34), penicillium (81) and aspergillus (112) and comprised 38 different species.