A major challenge in agricultural industry is the development of techniques that can screen plant materials for viroid infection.The microarray technique shows promise in this regard, as their high throughput nature can potentially detect a range of viroids using a single test.In this paper, we present a microarray that can detect a wide spectrum of all the 8 reported viroid genera including 37 known plant viroid species.The array was constructed using an automated probe design protocol which generated a minimal number of probes to detect viroids at the genus level.The designed arrays showed a high specificity and sensitivity when tested with a set of standard virus samples.Microarray screening was applied on an infected citrus sample.Hop stunt viroid infection was identified as the major disease causing pathogen for the infected citrus sample.