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In this study, we address the involvement of T. citricida in strain segregation and genetic bottleneck events by comparing the nucleotide diversity of CTV coat protein (CP) gene variants present in field-grown trees with that of variants retrieved from single apterous aphids. Plant material and aphids were collected in orange orchards in the northern part of Portugal. Shoots from two trees that were found to be positive using ELISA and twenty-four apterous aphids from these same trees were selected for individual molecular assays. CTV was detected in 60% of the aphids by amplification of a 417-bp fragment of the CP gene. Analysis of molecular variance (AMOVA) of this fragment revealed that most of the variation of the virus was found among individual aphids (FSC: 0.766) within each location. Nucleotide diversity comparison between the pool of sequences obtained from a given shoot and sequences …