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<i>Pinus bungeana</i>, an endangered and native coniferous tree species in China, has considerable timber and horticulture value. However, little is known about needle diseases in <i>P. bungeana</i>. A needle blight of <i>P. bungeana</i> has been observed in Hebei Province, China. <i>P. bungeana</i> inoculated with mycelial plugs of fungal isolates presented symptoms similar to those observed under field conditions. Ten virulent fungal isolates were identified as a small-spored <i>Alternaria</i> species based on morphological observations. Maximum likelihood and Bayesian phylogenetic analyses carried out with multilocus sequence typing of eight regions (SSU, LSU, ITS, <i>gapdh</i>, <i>tef1</i>, <i>Alt a 1</i>, <i>endoPG</i>, OPA10-2) assigned the pathogen to <i>Alternaria alternata</i>. This is the first report of <i>A. alternata</i> causing needle blight on <i>P. bungeana</i> in China.