The interaction between P. indica and A. thaliana results in growth promotion and enhanced seed production. I studied the role of various P. indica-released factors in the interaction and the signalling pathways they activate. We describe the isolation of a growth-promoting factor from the cell wall of P. indica. The cell wall extract (CWE) induces a transient cytosolic Ca2+ elevation in the roots of Arabidopsis and tobacco plants expressing the Ca2+ bioluminescent indicator aequorin. The CWE and the fungus induce a similar set of genes in Arabidopsis roots, among them are genes with Ca2+ signalling-related functions. The CWE does not promote growth of P. indica insensitive lines and the growth promotion is abolished if the Ca2+ inhibitor BAPTA is added. The cellular Ca2+ elevations and are thus crucial for growth promotion, and Ca2+ signalling pathways are activated by incoming fungus. The CWE does not stimulate H2O2 production and the activation of defence gene expression, although it led to phosphorylation of mitogen-activated protein kinases (MAPKs) in a Ca2+-dependent manner. Thus, Ca2+ is likely to be an early signalling component in the mutualistic interaction between P. indica and A. thaliana similar to other interactions like AM symbiosis. P. indica releases isopentenyl-adenine (iP) and cis-Zeatin (cZ)-type cytokinins into axenic cultures, but elevated levels of cis Zeatin (cZ) isomers accumulate in colonized roots. However, our data clearly demonstrate that trans-zeatin (tZ) biosynthesis in Arabidopsis is required for the beneficial interaction as knocking out atipt1 atipt3 atipt5 atipt7 genes required for (tZ) biosynthesis results in no response to the fungus. The double mutant cre1ahk2 shows no growth response to P. indica. The CRE1 AHK2 receptor combination is thus crucial for the response to P. indica.