ABSTRACT. We developed a new system for detection of whole-genome differentiation using DNA-DNA hybridization, and tested its sensitivity with three closely-related Fusarium species. We compared DNA-DNA relatedness to nucleotide sequence homologies of five genetic regions between each of five strains of three Fusarium species. DNA-DNA relatedness by our system was 16.2-86.6%. Sequence homologies of 18S rDNA, rDNA cluster region from ITS1 to 28S rDNA, β-tub, EF-1α and lys2 were 100.0, 99.0-100.0, 96.7-100.0, 95.1-99.4, and 94.7-100.0%, respectively. Our system could clearly detect differentiation between closely-related fungal species which have very similar morphological-characteristics, and exhibit little diagnoses in nucleotide sequences. Our results suggest that this system is a good tool for identification and phylogenetic analysis of closely-related fungal species. A microbial species concept has been defined on the basis of whole-genome sequence relatedness, which corresponds well with biological relatedness (bacteria: [13]; yeast: [10]). In previous studies on genetic distances between closelyrelated fungal species and identification of fungal isolates [18], whole-genome sequence relatedness was measured using a DNA-DNA hybridization technique (DNA-DNA relatedness). In DNA-DNA hybridization experiments, DNA probes are generally labeled with radioisotopes or biotin. Recently, digoxigenin (DIG) has been used for the nonradioactive labeling of DNA probes. In a study performed to detect amplified virus DNA, sensitivity of the DIG-labeled probe was equivalent to that of a radioactive probe, and has a clearly higher sensitivity than that of a photobiotinylated probe [11]. Assays for DNA-DNA relatedness using the DIG system were performed with dot-blot hybridization on nitrocellulose membranes [15]. On the other hand, the 96-well microplate technique has been developed as a convenient method for binding DNAs in DNA-DNA hybridization. In this technique, a probe is hybridized with unlabeled DNA bound on the surface of microplate wells. This new technique has been used in systematics and for the identification of bacteria [4]. However, all previous studies using this technique were performed with photobiotinylated probes, which have low sensitivity of detection, as described above, and none of the studies were performed with fungal DNAs.Fusarium species are one of the most important fungi, well known as human, animal, and plant pathogens. They cause infectious diseases of the eye and opportunistic mycosis for humans and animals [8]. Furthermore, they produce many kinds of mycotoxins, T-2 toxin, nivalenol, fumonisin, and others. Mycotoxicoses are caused in the world by the contaminated food and feed [9]. Therefore, rapid and accurate identification of Fusarium species is essential in the fields of medicine and food hygienics. The detection of species-specific differentiation among Fusarium species using nucleotide sequence homologies of certain genes is sometimes difficult because of the little diagnoses in sequence...