In recent years, virus-induced gene-silencing (VIGS) has shown to be a powerful reverse genetics tool for gene function study. In this paper, an effective and persistent virus-induced gene silencing (VIGS) system was established with barley stripe mosaic virus (BSMV) for Haynaldia villosa. Examination of GFP gene expression showed that the BSMV vector moved systemically from leaf to leaf in inoculated H. villosa plants. This vector, expressing a cDNA fragment of phytoene desaturase (PDS), suppressed the transcript level of endogenous Hv-PDS gene as early as 6 days after inoculation, and caused photobleaching symptoms mainly on the newly developed upper leaves. Moreover, PDS gene silencing phenotype persisted through the whole growing period in H. villosa. With this established VIGS system, function analysis of a powdery mildew resistance related gene Hv-LRR was successfully performed. This is the first report that BSMV can be used for VIGS in a wild relative species of wheat. The established VIGS system will be a powerful reverse genetics tool for gene function study in H. villosa, an important genetic resource for wheat breeding.