Citrus tristeza virus (CTV), a brown citrus aphid (Toxoptera citricidus) transmitted, longest known plant virus belonging to the genus Closterovirus (Family: Closteroviridae) causes decline of different citrus species worldwide. It has a significant threat on citriculture of Northeast (NE) India. Assam lemon (Citrus lemon) orchards in four districts of Assam and two districts of Meghalaya were surveyed during the month of October-November of 2022 to study the disease incidence and genetic diversity of CTV infecting Assam lemon orchards. The tender twig samples from apparently infected of healthy Assam lemon tree were collected, brought to laboratory and analyzed. Based on Direct antigen coated-enzyme link immunosorbent assay (DAC-ELISA) and Polymerase chain reaction (PCR) it was found that 76.3% of the Assam lemon plants tested was infected by CTV. Fourteen CTV isolates infecting Assam lemon plants were characterized based on analysis of complete coat protein (CP) gene (672 nt) of the virus. The gene was amplified, cloned, sequenced and analyzed. Pairwise sequence analysis showed that the present isolates shared 88-100% nt identity among them and also other Indian and international CTV isolates compared. In phylogenetic tree, the present CTV isolates segregated into three genotypes; eight isolates fell in Indian CTV genotype TK1/K5, four isolates in Indian decline inducing CTV genotype Kpg3, and two isolates in Israel severe CTV genotype VT. Intra-farm genetic diversity among CTV isolates were observed in Assam lemon orchards. Recombination events in CP gene of the present CTV isolates were identified. Of several Assam lemon plants, four plants were identified as CTV free and maintained on healthy rough lemon root stock through grafting. Implementing clean plant certification program is the most important strategy for management of CTV by using virus free Assam lemon scion bank.