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The differential solvent extraction and further purification of fractions of endophytic Alternaria sp. isolated from Pinus ponderosa led to the isolation of further two perylenequinone compounds as 3,6,6a,9,10-pentahydroxy-7,8-epoxy-4-oxo-4,5,6,6a,6b,7,8,9-octahydroperylene (1) and 3,6,6a,7,10-pentahydroxy-4,9-dioxo-4,5,6,6a,6b,7,8,9-octahydroperylene (2). Structure of compounds 1–2 was determined on the basis of detailed spectroscopic analysis, as well as by comparison with literature reports. The antimicrobial, antileismanial, antimalarial and cytotoxic activities of compound 1 and 2 were evaluated.