In Croatia tobacco transplants are produced in greenhouses using the float tray system. The high plant density and high moisture provide extended periods of leaf wetness and promote development and spread of seedling diseases such as Rhizoctonia stem rot, Pythium root rot, Sclerotinia collar rot, Botrytis grey mould and blue mould. On the other hand, transplant production using sterile substrates significantly reduce the occurrence of disease in the initial stages of development. Notwithstanding the above, every year in transplant production we find plants with disease symptoms. The aim of this study was to identify pathogens that cause transplant damping-off. With the aim of identifying pathogens in the transplant production, we collected the young plants with disease symptoms during three years (2012-2014). Plant parts with symptoms were washed in running water, disinfected in a 96% ethanol and rinsed in sterile distilled water. Prepared plant parts were placed in Petri dishes with PDA and incubated in thermostat. Identifications were based on the mycelial growth rate, colony pigmentation, density of mycelia, presence or absence of spores and sclerotia and their morphology. In 2013 year we determined the occurrence of Sclerotinia sclerotiorum Lib. (de Bary) (causing agent of Sclerotinia collar rot), and in 2014 and 2015 years Botryotinia fuckeliana (de Bary) Whetzel (anamorph Botrytis cinerea Pers ex Fr.) (causing agent of Botrytis grey mould). Both pathogens affect a large number of plant species and their appearance is expected in the production of tobacco transplants in areas with well-developed agricultural production of field crops, vegetables, fruits and grapevine. Their appearance in the greenhouses is a consequence of the airborne spread of B. cinerea conidia and S. sclerotiorum ascospores. Soil borne pathogens (e.g. Pythium sp., Rhizoctonia sp.) have not been detected and due to the use of sterile substrates we in fact do not expect their appearance.