AbstractOne of the most pervasive plant viruses, the cucumber mosaic virus (CMV), Bromoviridae: Cucumovirus, infects a variety of plants worldwide and significantly affects production quality and quantity. Viral infection exhibiting severe mosaic and stunting symptoms in plants infected with turnip mosaic virus was observed in experimental fields in IARI. Leaf samples were collected and the virome was identified through high‐throughput sequencing subjecting ribosomal RNA‐depleted mRNA. Here, we unravel for the first time the complete genome sequences of two CMV isolates infecting yellow and black‐seeded mustard in India. The three segments of the viral genome, as well as coat protein cds, were amplified and subjected to Sanger sequencing. The three viral genomic components were 3348 of RNA1, 3032 and 3040 of RNA2, 2260 and 2236 nts of RNA 3, respectively (including the 5′ and 3′ UTR). The two isolates shared high sequence identity and clubbed with the subgroup‐IB isolates in a clade. Recombination signals were detected within all the three RNAs of both New Delhi isolates wherein one of the parent isolates was reported to infect the family Brassicaceae. Recombination was observed throughout the region of RNA2 but the 3′ UTR was observed to be most prone to recombination. This is the first comprehensive depiction of a recombinant CMV subgroup IB isolate from black, yellow and brown‐seeded mustard from India, which has implications for its robust detection and overall management. This study also provides insight into population structuring, host expansions, level of genetic heterogeneity and variability of worldwide prevalent CMV isolates.