Pepper (Piper nigrum L.) root rot caused by Fusarium solani f. sp. piperis (FSP; teleomorph: Nectria haematococca f. sp. piperis) includes two symptom types called root rot (RR) type and stem rot (SR) type. In this study, the temporal and spatial associations between perithecial formation of FSP and development of SR were investigated in naturally infested fields to verify the hypothesis that ascospores from the perithecia are the major inoculum source of the SR type on vines in the field. In surveys of all vines in two neighboring pepper fields every month from December 2005 to November 2006, I mapped the locations of all vines with perithecia and all vines the SR type. The frequency of vines with perithecia increased during April and May, the late rainy season. In June, the early dry season, the number of vines with SR type greatly increased. The vertical range of perithecial formation on the vines extended to 200 cm in height, but was restricted to 30 cm in the dry season in both fields. The join-count statistics showed a significant spatial association between vines with perithecia and vines with SR type in one field (P = 0.042), while no significant spatial association was recognized in another field. The results suggested that ascospores from perithecia of FSP on pepper vines are likely to be one of the main inoculum sources of the SR type of the disease on adjacent vines, but they may not be the exclusive source.