In searching for symbionts derived from bioactive natural products, six sulfureous diketopiperazines designated as lasiodiplines A-F (1-6) were characterized from the culture of Lasiodiplodia pseudotheobromae F2, previously residing in the apparently normal flower of Illigera rhodantha (Hernandiaceae). Identification of structures was accomplished by a combination of spectroscopic and computational approaches, in conjunction with the low-temperature (100K) single-crystal X-ray diffraction with Cu Kα radiation. Lasiodipline E (5) was demonstrated to be antibacterial against the clinical strains Streptococcus sp., Bacteroides vulgates, Peptostreptococcus sp. and Veillonella parvula, respectively, with an minimum inhibitory concentration (MIC) range of 0.12-0.25 μg/mL. In addition, compounds 4 and 6 exemplify two unusual architectures of natural cyclodipeptides, signifying the unique biochemical characteristics of the producing fungus.