Abstract We give direct evidence of distinct quantum dot states clustered but also spatially separated in single GaN islands. Resulting from GaN layer growth on top of AlN, the islands are predominantly formed in close vicinity to threading dislocation bundles. Detailed analysis of the inner optical and structural properties, performed by nanoscale cathodoluminescence, reveals various sharp quantum dot emission lines from different regions in an otherwise continuous island. Thickness fluctuations found within these islands are made responsible for the clustering of quantum dot states.