The pecan (Carya illinoinensis) industry in South Africa is growing rapidly, and it is becoming increasingly crucial to understand the risks posed to pecans by fungal pathogens. Black spots on leaves, shoots, and nuts in shucks caused byAlternariaspecies have been observed since 2014 in the Hartswater region of the Northern Cape Province of South Africa. Species ofAlternariainclude some of the most ubiquitous plant pathogens on earth. The aim of this study was to use molecular techniques to identify the causative agents of Alternaria black spot and seedling wilt isolated from major South African pecan-production areas. Symptomatic and non-symptomatic pecan plant organs (leaves, shoots, and nuts-in-shucks) were collected from pecan orchards, representing the six major production regions in South Africa. ThirtyAlternariaisolates were retrieved from the sampled tissues using Potato Dextrose Agar (PDA) culture media and molecular identification was conducted. The phylogeny of multi-locus DNA sequences ofGapdh,Rpb2,Tef1, andAlt a 1genes revealed that the isolates were all members ofAlternaria alternata sensu stricto,forming part of theAlternaria alternataspecies complex. The virulence of sixA. alternataisolates were tested on detached nuts of Wichita and Ukulinga cultivars, respectively, as well as detached leaves of Wichita. TheA. alternataisolates were also evaluated for their ability to cause seedling wilt in Wichita. The results differed significantly between wounded and unwounded nuts of both cultivars, but not between the cultivars. Similarly, the disease lesions on the wounded detached leaves were significantly different in size from the unwounded leaves. The seedling tests confirmed thatA. alternatais pathogenic and thatA. alternatacauses black spot disease and seedling wilt of pecans. This study is one of the first documentations of Alternaria black spot disease of pecan trees and its widespread occurrence in South Africa.