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The results of a mycological monitoring, carried out from 2001 until 2003 in two forest reserves (in the Bükk and the Mecsek Mountains) within the frame of a project of the Hungarian Biodiversity Monitoring System (HBMS) aiming to monitor forest reserves and managed forests, are presented. Standard sampling method had to be developed and methods of data analysis (a so-called protocol) had to be elaborated for monitoring activities.