The diploma thesis deals with the material survey of wooden elements of the structures of two medieval castles Krásna Hôrka and Slovenská Ľupča.These are two significant National Cultural Monuments with a very rich history that we have carried out sampling for in-situ surveys to develop microscopic analyzes to determine the species of plants and the overall health status of the sites. The work is also aimed at verifying the historical protective coating of the ceiling construction in the castle vestry NCM Slovenská Ľupča.The research maps the history of the sites, the method of processing the collected samples and their overall survey, enriched with SEM microscope images, which are evidence of the occurrence of various microorganisms in the individual elements of the structures. At the same time, we are addressing this issue with any protective measures that can help to preserve the objects for future generations as well.