Plants activate an immune or symbiotic response depending on the detection of distinct signals from root-interacting microbes. Both signalling cascades involve Ca 2+ as a central mediator of early signal transduction. In this study, we combined aequorin- and cameleon-based methods to dissect the changes in cytosolic and nuclear Ca 2+ concentration caused by different chitin-derived fungal elicitors in Lotus japonicus roots. Our quantitative analyses highlighted the dual character of the evoked Ca 2+ responses taking advantage of the comparison between different genetic backgrounds: an initial Ca 2+ influx, dependent on the LysM receptor CERK6 and independent of the Common Symbiotic Signalling Pathway (CSSP), is followed by a second CSSP-dependent and CERK6-independent phase, that corresponds to the well-known perinuclear/nuclear Ca 2+ spiking. We show that the expression of immunity marker genes correlates with the amplitude of the first Ca 2+ change, depends on elicitor concentration and is controlled by Ca 2+ storage in the vacuole. Our findings provide an insight into the Ca 2+-mediated signalling mechanisms discriminating plant immunity- and symbiosis-related pathways in the context of their simultaneous activation by single fungal elicitors.