Phytophthora root rot (PRR), caused by Phytophthora cinnamomi, is one of the most devastating avocado diseases worldwide. We previously reported a group of genetically distinct, more virulent, and less fungicide-sensitive isolates corresponding to the A2 clade II clonal population in southern avocado-growing regions in California that may have originated from Mexico. To test this hypothesis, we assessed the genetic and phenotypic diversity of the California and Mexico avocado P. cinnamomi populations. We found that P. cinnamomi populations in these two locations belong to the two previously described A2 clades. Higher genetic differentiation was detected among Mexican isolates when compared with the populations from California; however, most Mexican isolates clustered with the California A2 clade II populations, providing evidence for the Mexican origin of these isolates in southern avocado-growing regions. With the exception of one diploid Mexican isolate, all isolates were estimated to be triploid based on inferred allele ratios. Despite clonality, wide phenotypic variability was detected within and among populations regarding growth rate, optimal growth temperature, fungicide sensitivity, and virulence. Interestingly, contrasting virulence patterns were found depending on the host and infected tissue utilized. This study reveals the adaptative capacity of clonal P. cinnamomi populations to local environments and control methods. Pathogen migration between Mexico and California was also inferred, which highlights a pathway that should be surveilled if further emergence is to be avoided. Monitoring and characterizing the P. cinnamomi populations is critical to developing effective and durable PRR control methods to ensure the sustainability of the avocado industry worldwide. [ ] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Mexico is the world’s leading producer of avocado (Persea americana); however, its productivity is threatened by various diseases, especially root rot caused by Phytophthora. While P. cinnamomi is the most commonly reported species worldwide, this study identified P. mengei for the first time as a causal agent of root rot and trunk canker in avocado orchards in the state of Michoacán, México. The morphological and molecular characterization of four isolates (three from canker and one from root rot) confirmed their identity: semi-papillate sporangia and plerotic oospores with paragynous antheridia, with sequence identities of 99.87% (ITS) and 100% (COI) with type sequences of P. mengei. Pathogenicity tests demonstrated the ability to infect roots, stems, and fruits, although with a low reisolation percentage in roots (10%), suggesting an opportunistic pathogen behavior. Sensitivity tests to potassium phosphite (EC₅₀ of 3.67 μg/mL⁻¹ a.i.) and metalaxyl-M (0.737 μg/mL⁻¹ a.i.) revealed possible limitations for chemical control. These findings position P. mengei as an emerging pathogen with important implications for integrated crop management. To the best of our knowledge, this is the first report of P. mengei causing root rot and trunk canker in avocado in Michoacán, Mexico.