Fusarium wilt is a serious fungal disease in pigeonpea (Cajanus cajan) which causes severe yield loses (up to
90%). Genetic diversity in pigeonpea wilt pathogen [Fusarium udum (fud)] was characterised using 14 isolates
collected from major pulse growing regions of India. Twenty four RAPD primers generated a total of 226 bands
(ranging 0.3 to 3.0 kb) in F. udum with an average of 9.4 bands per primer and a total of 27 alleles were produced
by twelve SSR primers with an average of 2.25 alleles per marker. All isolates amplified a single band ranging from
100 to 450 bp. The universal ITS primer pair amplified 650 bp bands in all fourteen fud isolates, while significant
length polymorphism was obtained only when analysed by restriction digestion with EcoRI and Hind III
enzymes. Cluster analysis of ITS-RFLP grouped all 14 Fud isolates into three major clusters. Cluster analysis
using various markers showed the grouping of Fusarium isolates strictly according to their cultural characteristics
and degree of pathogenicity and not the geographical origin. This information will be helpful for pathologists and
plant breeders to design effective resistance breeding programmes in pigeonpea taking into account the diversity
in wilt pathogen.