In recent years, research has focused on phenolic compounds and their putative role as markers of graft incompatibility. Thus far, no studies have been conducted on the role of phenolic compounds in chestnut (Castanea spp.). The present study investigated the content of phenolic compounds in different combinations of Castanea spp. cultivars and rootstocks. Analyses were performed on the inner and outer tissues of chestnut grafts at two phenological sampling stages. The separation, identification and quantification of the phenolic markers via HPLC were preceded by an ultrasonic green extraction. Two chromatographic methods were tested for a total of 15 phenol compounds. Flavonol compounds were not detected, while cinnamic acids were found in low concentrations. The amount of gallic acid turned out to be higher at the graft union of the incompatible combination (20.11 ± 1.47 mg/100 gFW vs. 8.94 ± 1.08 mg/100 gFW). The same pattern was observed for catechin (15.79 ± 1.83 mg/100 gFW vs. 9.63 ± 1.98 mg/100 gFW). Differences in tannin concentrations seemed to be species-specific, and were apparently not related to graft incompatibility. The present work underlines the potential application of certain phenol compounds for the early prediction of graft incompatibility in Castanea spp.