The regulation capacity of four humic substance (HS) samples, a soil humic acid (HA) and two HAs and one fulvic acid (FA) isolated from a composting substrate, was evaluated at two concentrations on the growth in vitro of one plant pathogenic, Sclerotinia sclerotiorum, and two antagonistic, Trichoderma viride and T. harzianum, soil-borne fungi. The presence of any HS sample in the growing medium, especially those from the composting substrate, caused a relevant inhibition of the mycelial growth of S. sclerotiorum and a marked stimulation of sclerotial formation that was exhibited as early appearance and numerical increase. On the contrary, the same HS treatments generally did not inhibit the growth of the two Trichoderma species. In particular, T. viride was significantly stimulated by any HS sample at any concentration, with the only exception of HA from fresh-composting substrate, whereas T. harzianum appeared to be stimulated only slightly or not significantly influenced. Only S. sclerotiorum showed evident high correlations of both the extent of the inhibitory action on mycelial growth and the final number of sclerotia with some chemical and functional properties of HS, such as total acidity, COOH group content, and elemental composition.