Papaya (Carica papaya L.) is grown on approximately 16,000 ha in Mexico. In August 2014, a fruit rot was observed on papaya fruit grown in Colima, Mexico. Disease symptoms included an initial soft rot, and then the production of profuse mycelial growth with light-brown to dark sporangia on the infected fruit. Fungal colonies on potato dextrose agar (PDA) grew rapidly at 1.4 cm/day at 25°C. Morphological characteristics include coenocytic mycelia, spherical sporangia 86.31 μm (69.23 to 146.20 μm) with a persistent wall covered with crystalline spines. Sporangia split longitudinally into two halves to release the spores, were columellae obvoid, 58.84 (31.24 to 88.57) × 49.71 (32.15 to 71.65) μm; and sporangiospores were smooth, mainly ellipsoid, hyaline, unicellular, 8.37 (5.54 to 10.99) × 6.52 (4.43 to 9.06) μm (n = 100) with hyaline filiform appendages arising from the ends of the spores. The cardinal temperatures were 10, 25, and 40°C. Based on these morphological characteristics, the fungus was identified as Gilbertella persicaria (Eddy) Hesseltine (Benny 1991). The sequences of the internal transcribed spacer (ITS) of ribosomal DNA and the D1-D2 region of the large subunit (LSU) were amplified with primers ITS1-ITS4 and NL1-LR3 (Walther et al. 2013) from a representative isolate (HP12) of this fungus, and submitted to GenBank (Accession Nos. KR076757 and KR076760, respectively) and showed 100% sequence identity with Gilbertella persicaria Accession Nos. JN206224 and JN206517, respectively. Pathogenicity of the isolate HP12 was tested by spraying 10 ml of a sporangiospore suspension (5 × 105 sporangiospores/ml) onto three healthy papaya fruits cv. Maradol previously disinfested and wounded with a fine needle. The control fruit were sprayed only with sterilized distilled water. All fruit were maintained in plastic boxes at 25°C with 80% relative humidity. The experiment was conducted twice. Initial symptoms of the disease appeared as water-soaked spots at 24 h, then white mycelia was observed at 48 h, and light brown to dark sporangia were observed at 72 h after inoculation. The pathogen was reisolated from the margins of the lesions, fulfilling Koch’s postulates. Control fruit remained healthy. G. persicaria has been reported causing fruit rot on peaches (Ginting et al. 1996), dragon fruit (Guo et al. 2012), and black plum (Pinho et al. 2014). To our knowledge, this is the first report of G. persicaria causing fruit rot of papaya worldwide. © 2016, American Phytopathological Society. All rights reserved.