Fusarium wilt becomes a serious problem in isabgol growing agro climatic zones of Rajasthan. This study was undertaken to identify and characterisation through morphological, cultural and to determine the genetic diversity of isolates of Fusarium oxysporum. Among the isolates, maximum growth and sporulation was recorded in UDP Fo-1 showed 90 mm colony diameter with whitish orange irregular fluffy growth with yellowish pigmentation and 4.20x106 conidia/mm2 sporulation. Whereas Isolate SRH Fo-1 showed minimum growth 65.0 mm colony diameter with white plenty mycelium irregular growth with light yellow pigmentation with 2.2x106 conidia/mm2. Molecular characterisation based on the reproducibility of the PCR amplification. RAPD is an effective tool to differentiate geographically and genetically isolated populations. The PCR result from 10 RAPD primers was repeated three times to assess reproducibly. By using 10 RAPD primers, a total of 112 reproducible bands were amplified, out of which 88 (78.5%) were polymorphic and 24 (21.42%) were monomorphic. Similarity coefficient among the isolates ranged from 1.9 per cent (CHI Fo-1 and UDP Fo-1) to 74.6 per cent (PRA Fo2 and CHI Fo1). Genetic similarity coefficient was found relatively low among all the isolates, which ranged from 0.012 to 0.74. The maximum similarity value (0.746) was obtained between isolates PRA Fo2 and CHI Fo1, both of which belong to Pratapgarh and Chittorgarh.