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Plants are continuously exposed to beneficial and pathogenic microbes, but how plants recognize and respond to friends ver- sus foes remains poorly understood. Here, we compared the molecular response of Arabidopsis thaliana independently chal- lenged with a Fusarium oxysporum endophyte Fo47 versus a pathogen Fo5176. These two F. oxysporum strains share a core genome of about 46 Mb, in addition to 1,229 and 5,415 unique accessory genes. Metatranscriptomic data reveal a shared pattern of expression for most plant genes (about 80%) in responding to both fungal inoculums at all timepoints from 12 to 96 h postinoculation (HPI). However, the distinct responding genes depict transcriptional plasticity, as the path- ogenic interaction activates plant stress responses and sup- presses functions related to plant growth and development, while the endophytic interaction attenuates host immunity but activates plant nitrogen assimilation. The differences in reprogramming of the plant transcriptome are most obvious in 12 HPI, the earliest timepoint sampled, and are linked to accessory genes in both fungal genomes. Collectively, our results indicate that the A. thaliana and F. oxysporum interac- tion displays both transcriptome conservation and plasticity in the early stages of infection, providing insights into the fine- tuning of gene regulation underlying plant differential responses to fungal endophytes and pathogens.