Technical Abstract: Phylogenetic analysis of the full or partial genomic sequences of the Citrus tristeza virus (CTV) isolates T36, T68-1 and NS25 showed phylogenetic incongruities between sequences involved in viral RNA replication and those involved in movement and other viral functions. This incongruity was not found for these sequences for isolates T3, T30, T385, VT and T318A. Distance analysis of the replication sequences of T36, T68-1 and NS25 showed these are phylogenetically distinct from each other and from replication sequences of isolates T3, T30, T385, VT and T318A, which formed a cluster of related sequences. Sequences not directly associated with replication were highly similar among all CTV sequences examined. Potential recombination points were identified in the genomes of T36, T68-1 and NS25, indicating that recombination joined disparate replication sequences with highly conserved sequences for movement and other viral functions. The evidence suggests that the CTV genome has evolved two gene modules. Large increases in genetic diversity have occurred in the replication module when distantly related replication sequences were introduced into infected citrus trees and recombination occurred with the more conserved sequences of a CTV population already present in these trees. Sequence conservation in the movement/encapsidation module may be linked to the virus’ adaptation and restriction to citrus.