Approximately 1700 naphthoquinones have been reported from a range of natural product source materials, but only 283 have been isolated from fungi, fewer than 75 of those were dimers, and only 2 were heterodimers with a head-to-tail linkage. During a search for anticancer leads from fungi, a series of new naphthoquinones (1-4), including two heterodimers (3 and 4), were isolated from Pyrenochaetopsis sp. (strain MSX63693). In addition, the previously reported 5-hydroxy-6-(1-hydroxyethyl)-2,7-dimethoxy-1,4-naphthalenedione (5), misakimycin (6), 5-hydroxy-6-[1-(acetyloxy)ethyl]-2,7-dimethoxy-1,4-naphthalenedione (7), 6-ethyl-2,7-dimethoxyjuglone (8), and kirschsteinin (9) were isolated. While the structure elucidation of 1-9 was achieved using procedures common for natural products chemistry studies (high-resolution electrospray ionization mass spectrometry (HRESIMS), 1D and 2D NMR), the elucidation of the heterodimers was facilitated substantially by data from the long-range heteronuclear single quantum multiple bond correlation (LR-HSQMBC) experiment. The absolute configuration of 1 was established by analysis of the measured vs calculated ECD data. The racemic mixture of 4 was established via X-ray crystallography of an analogue that incorporated a heavy atom. All compounds were evaluated for cytotoxicity against the human cancer cells lines MDA-MB-435 (melanoma), MDA-MB-231 (breast), and OVCAR3 (ovarian), where the IC50 values ranged between 1 and 20 μM.