Fusarium oxysporum f. sp. lycopersici (FOL) races and F. oxysporum f. sp. radicis lycopersici (FORL), the causal agents of root rot and crown rot diseases, respectively, cause serious economic losses in tomato greenhouses where production is intensive in the West Mediterranean region of Turkey. The isolates were collected from West Mediterranean region of Turkey and were characterized by specific primers based on three races (r1, r2, r3), besides pathogenicity tests in in vivo conditions Additionally, a scheme was developed using newly tested ISSR and SRAP markers to a genotyping database and to determine the possible origin of these pathogens. The present study provided new information on these pathogens based on their races and their dominant existence in this region that has not been reported before. Genetic diversity detected in the same races of the pathogen may be associated with difficulties in controlling the pathogen and a possible resistance formation effort exerted by the pathogen to chemicals used in plant protection in tomato greenhouses. Molecular analyses indicated genetic diversity in pathogen isolates identified as r3, r2 and FORL, which may be associated with abiotic stress to which the pathogens were exposed. (C) 2009 Elsevier Ltd. All rights reserved.