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Citrus producers in many countries are facing serious problems with the emergence of citrus huanglongbing (HLB). This study was conducted to 1) detect the HLB pathogen complex in Upper Awash citrus production areas; 2) detect the presence of insect vectors of the pathogen and 3) understand the relationship between huanglongbing and nutritional profile of citrus. Leaf samples were collected from symptomatic orange and mandarin trees. Insect were collected using sticky trap and stem-Tap sampling techniques. Total DNA was isolated from leaves. Real time PCR was used to screen for the presence of ‘Candidatus Liberibacter’ species while conventional PCR was done to detect particular species. Field history was recorded for nutrient deficiency and amendments, as well as symptoms associated with deficiency. Leaf tissue analysis was conducted to quantify the level of different elements in HLB infected and none infected samples. All citrus species and varieties were found to be vulnerable to HLB infection. The result was verified by real time PCR that indicated the presence of ‘Ca. Liberibacter’ species. All conventional PCR tests indicated the presence of ‘Ca. Liberibacter asiaticus’. No other species were detected in the samples. The pathogen was primarily transmitted by pruning materials and Diaphorina citri. The pathosystem was associated with nutrient deficiency such as decrease in zinc in which the management has shown to aggravate the disease pressure. The study provided insights on the distribution, insect vector and nutritional profiles of HLB infection on citrus trees. Future studies should focus on other marker data to determine the nature of origin and variability of this important citrus pathogen in Ethiopia.