For molecular characterization of F1 hybrid of 0. sativa x 0. officinalis and its backcross-I generation (BC1) with 0. sativa through genomic in situ hybridization (GISH), biotin labelled total genomic DNA from 0. officinalis was used as probe. Cytological preparations were made by enzymatic maceration technique. Probe was hybridized onto chromosomal preparations at 37°C and signals were detected by colorimetric method using 3-amino-9-ethylcarbazole. Labelling efficiency of probe was determined by dot blot method prior to hybridization reaction. Based on the appearance of signal on chromosomes, it was inferred that there exists partial homoeology between the genomes of 0. sativa and 0. officinalis and there are higher chances of gene(s) transfer from 0. officinalis to 0. sativa . More over the study shows that GISH is a powerful technique for genomic characterization of breeding material at any generation.