Increased mortality rates in Scots pine (Pinus sylvestris) forests have recently been observed in the inner alpine Swiss Rhone valley. Drought, in combination with stand competition, mistletoe infections as well as nematode and insect infestations, appears to be the main factor for the decline. In focus of this study was the occurrence and role of fungal pathogens in the decline dynamics. Branches, stems and roots of 208 trees in five different crown transparency classes were collected and inspected for blue stain and fungal infections. Neither Armillaria species nor Heterobasidon annosum s. str. were detected, but blue stain was commonly observed. Visible blue stain increased with increasing crown transparency. Among the recently dead trees, 80% showed visible blue stain in the branches, 90% in the roots and 100% in the stems. In the crown transparency classes 2 and 3 (25–60% crown transparency), five of the 103 trees showed visible blue stain in the roots, one of 130 trees in the stem but none in the branches. Blue-stain fungi were isolated from all parts of the trees and from all crown transparency classes. Overall incidence of blue stain was highest in the roots and lowest in the branches. In class 2, roots of 60% of the trees were visibly blue-stained or developed blue stain in culture, but stems of only 24% and branches of 14% of the trees. In the roots Leptographium species, mostly L. serpens, dominated. From stems and branches, mainly Ophiostoma species were isolated. The positive relationship between the incidence of blue stain and crown transparency, in combination with the high infection levels of roots of fairly vigorous Scots pines, indicates the pathogenic potential of the blue-stain fungi. Hence, these fungi together with their insect vectors may well act as an important contributing factor involved in pine decline.