ABSTRACT: The nature of many microbe-host interactions is not static, but may shift along a continuum from mutualistic to harmful depending on the environmental conditions. In this study, we assessed the interaction between the foundation plant eelgrass Zostera marina and the frequently associated protist Labyrinthula zosterae. We tested how an important environmental factor, nutrient availability, would modulate their interaction. We experimentally infected naive eelgrass plants in combination with 2 nutrient levels (fertilized and non-fertilized). We followed L. zosterae infection, eelgrass growth parameters and host defense gene expression over 3 wk in large 600 l tanks. Inoculation with L. zosterae and nutrient limitation both reduced eelgrass growth. These effects were additive, whereas no interaction of nutrient treatment and L. zosterae inoculation was detected. Gene expression levels of 15 candidate genes revealed a reduced expression of photosynthesis-related genes but an increased expression of classical stress genes such as Hsp80 in inoculated plants 2 d post-inoculation. However, we found no effects on plant mortality, and plants were able to clear high infection levels within 3 wk to ambient background levels of infection as assessed via specific RT-qPCR designed to quantify endophytic L. zosterae. Thus, we found no evidence that L. zosterae is a facultative mutualist that facilitates eelgrass growth under nutrient-limiting conditions. We suggest that the interaction between contemporary L. zosterae genotypes and Z. marina represents a mild form of parasitism in northern Europe because the damage to the plant is moderate even under nutrient limitation stress.