Successful endophytic plant-fungal interactions such as arbuscular mycorrhizal fungal  (AMF) associations are increasingly recognized not only as beneficial to host plants, but also as the critical link that establishes a continuum between plant and soil. Through this linkage, the association plays an important role in soil aggregate stabilization and consequent organic C and N storage. In particular, the large hyphal networks produced by AMF associations are thought to stabilize aggregates through the combined action of the extraradical hyphae and hyphal exudates including glomalin-related soil protein (GRSP). Different crops vary in their AMF dependence and thus it is expected that crop rotations may significantly affect GRSP production and related soil water-stable aggregation.  Our objectives were to assess the impact of crop rotation on GRSP and relate GRSP to soil quality indicators, including water aggregate stability and associated C and N. Although crop rotation affected total GRSP as determined by a Bradford assay, this did not translate consistently into significant differences in AMF-specific immunoreactive glomalin, determined using an ELISA technique. These results suggest that although crop rotation may affect the material extracted as GRSP, the origin of these proteins likely includes non-AMF sources. Irrespective of origin, GRSP contributes to water stable soil aggregation.