Seedlings of Calocedrus formosana, Chamaecyparis formosensis, Chamaecyparis obtusa var. formosana, Podocarpus costalis, Podocarpus macrophyllus, and Podocarpus nakaii are prone to various fungal infections while leaf blight and wither tip diseases caused by Pestalotiopsis sensu lato taxa are considered one of the major diseases in forestry nurseries and botanical gardens worldwide. As part of a survey on fungal diseases on aerial parts of the precious conifers in Taiwan, 66 Pestalotiopsis sensu lato strains were collected and Pestalotiopsis neolitseae, P. parva, P. subshorea, P. trachycarpicola, Pseudopestalotiopsis elaeidis, Ps. ixorae, and four tentative clades in Neopestalotiopsis were identified associated with leaf blight and wither tip diseases of six precious conifers in Taiwan. The species identification was based on both phenotypic characters and multi-locus phylogenies from the internal transcribed spacer (ITS), beta-tubulin (tub2), and translation elongation factor 1-α (tef1-α) and the species limits were determined based on the Genealogical Concordance Phylogenetic Species Recognition (GCPSR) principle, Poisson Tree Processes (PTP), Pairwise Homoplasy Index (PHI) test, Automatic Barcode Gap Discovery (ABGD) method, and Average Nucleotide Identity (ANI). Based on the results of pathogenicity assessments, Neopestalotiopsis group were identified as the major pathogens associated with leaf blight and wither tip diseases of with six precious conifers. According to our knowledge, P. subshorea and Ps. elaeidis were reported for the first time in Taiwan. This investigation delivers the first assessment of Pestalotiopsis sensu lato taxa related to leaf blight and wither tip on six precious conifers in Taiwan.