design: Total RNA was extracted from Citrus reticulata (Kinnow mandarin) leaf samples exhibiting virus-like symptoms. RNA quality was assessed using agarose gel electrophoresis and spectrophotometry. Ribosomal RNA was depleted, and sequencing libraries were prepared using a standard RNA-Seq library preparation kit. Libraries were sequenced on an Illumina platform using paired-end reads. The data were generated for virome analysis and identification of viral pathogens associated with Kinnow decline.