African citrus greening disease (ACGD) is considered as one of the major diseases of citrus threatening citrus production in East Africa. Our study aimed for the first time to assess the incidence, severity, and distribution patterns of ACGD in Kenya and Tanzania. In total, 105 citrus orchards were assessed in 13 regions representing low, mid, and high altitude areas. In each backyard and orchard, trees were randomly selected and rated for visual ACGD symptoms; then leaves and insect samples collected for analysis of ‘Candidatus Liberibacter africanus' (CLaf), the presumptive causal agent of ACGD. Endpoint PCR, sequencing, and molecular phylogenetic tools were employed to confirm the identity of potential circulating pathogens. Incidence and severity of ACGD varied significantly among the different regions. Both Trioza erytreae (Del Guerico) (Hemiptera: Triozidae) and the invasive Asian citrus psyllid vector Diaphorina citri (Kuwayama) (Hemiptera: Liviidae) were found to co-occur in upper and lower midland regions. Molecular characterization identified ‘Candidatus Liberibacter africanus spp. Clausenae’ (CLafCl) as the main causal agent of ACGD in most of the citrus plants and insect samples. No instances of Candidatus Liberibacter asiaticus infection were found. These findings provide valuable insights into understanding and management of ACGD by employing stringent and early disease detection tools to curb the spread of the disease.