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Castor (RicinusCommunis. L, 2n= 20) is crop of tropical, sub tropical and warm temperate regions. Castor is most promising crop for the commercial and medicinal values. In recent years castor production is lessen due to Macrophomina Phaseolina diseases outbreak which is a necrotrophic soil borne pathogen. Macrophomina Phaseolina diseases known as root rot which cause severe diseases especially in dry area. In India it can damage 80-100% crop. No effective controlling measures are mentioned till date for disease. The more practical practices to control the disease are to identify castor resistant genotype from the Macrophomina Phaseolina fungus. There is very less information regarding the molecular aspect of castor JI 357 and 48-1 respectively resistant and susceptible genotype. Thus, Resistant genotype of castor provides basis of utilization of molecular approach in the molecular study of resistant genes and mechanism of their gene expression to increase the resistant genotype of castor whereas susceptible genotype helps in the compare the expression and activity of gene. Genome sequencing of resistant and susceptible castor genotype was carried out in Ion Torrent (PGM), Next Generation Sequencer. The data obtained in which resistant sample posses total 2,651,111 reads with total 379,341,629 bases with the average read length of 143 bp with 8 lowest and 597 highest sequence length with 43% of GC content in resistant genotype and in susceptible total 124,860 reads were generated with total 16,681,708 bases with the average read length of 134 bp with 8 lowest and 572 highest sequence length with 54% of GC content …