Several Pinot noir (PN) (Vitis vinifera) clones grafted on 110 Richter (110R) (V. berlandieri x V. rupestris), a drought tolerant and phylloxera resistant rootstock, exhibit a necrotic graft union (NGU) that girdles the trunk leading to red canopy. To determine the causal agent of NGU, a bioassay was conducted using budwood from FPS 76, a PN clone released after microshoot tip culture of French clone PN 927, and from nine self-rooted PN 927 grapevines with history of NGU. Grafts of FPS 76 and PN 927 grapevines on 110R were established in a vineyard, in 2011 and 2012, respectively. In 2016, cambial scrapings were obtained from lignified canes of two composites from PN 927 budwood source, and from a PN grapevine with NGU in the same vineyard. Total RNA was extracted, barcoded cDNA libraries constructed after rRNA depletion, and subjected to Illumina sequencing. Sequence analysis revealed presence of Grapevine red globe virus (GRGV) and Grapevine rupestris stem pitting-associated virus (GRSPaV) in all three libraries. In 2018, observations on grafted grapevines revealed that 12 out of 23 grapevines of PN 927 had red canopy and the FPS 76 grapevines did not. RT-PCR tests conducted on the vines for GRBV and GRSPaV indicated that GRSPaV was the only virus present in all PN927 grapevines with red canopy but not in the asymptomatic grapevines. These results indicate that GRSPaV infection of PN 927 causes an incompatibility reaction leading to NGU when grafted on 110R.