The aim of this study was to investigate the differences between Castanea sativa Mill. and Castanea crenata Siebold & Zucc. × Castanea sativa Mill. in rooting ability in relation to endogenous levels of auxin, auxin cofactors and inhibitors that influence rooting success. Leafy cuttings of the two commercial cultivars 'Marsol' and 'Maraval' (Castanea crenata × Castanea sativa) and the native accession 'Kozjak' (Castanea sativa) were analyzed. Endogenous indole-3-acetic acid (IAA) concentration was assessed at the beginning of propagation (day 0); in addition, strigolactones, flavonoids, rooting ability and quality were assessed 120 days after. The concentration of endogenous IAA in 'Maraval' (324.34 ± 28.66 ng g-1) and 'Marsol' (251.60 ± 35.44 ng g-1) was significantly higher than in 'Kozjak' (112.87 ± 35.44 ng g-1). The best rooting result was observed with the genotypes 'Maraval' (100.00 ± 0.00%) and 'Marsol' (90.48 ± 6.15%). A significantly lower strigol concentration was observed in the roots of 'Maraval' (75.54 ± 17.93 ng g-1) compared with other genotypes. The total flavonoid concentration in 'Maraval' was significantly higher (2794.99 ± 187.13 μg g-1) than in 'Kozjak' (1057.38 ± 61.05 μg g-1). Our results indicate that the concentration of endogenous IAA has a significant influence on rooting success. The results further indicate that in the case of flavonoids and strigolactones, not only the individual compounds but also their ratio is important for rooting success. Correlation coefficients calculated between analyzed compounds and rooting success point toward specific functions of flavonoids and strigolactones in the rooting of Castanea that need to be functionally analyzed.