Huanglongbing (HLB) disease detection in Cuba in 2006 led to a turn in citrus management in the country, including the production of certified budwood in protected nurseries, eradication of symptomatic plants and old orchards, and chemical control of the vector Diaphorina citri. This dramatic shift in citrus farming could have affected the incidence and composition of citrus tristeza virus (CTV) populations. This work aimed to determine CTV incidence and characterize viral isolates from the main Cuban citrus-producing areas.