Non‐invasive functional exploration techniques can provide information on different aspects of general organism functioning and, unlike lethal or invasive techniques, allow individual organisms to be monitored for as long as necessary. For bivalves, a fairly wide variety of methods and instrumental means exist allowing physiology to be assessed on‐line while keeping animals alive and intact. The current range of non‐invasive techniques for bivalves consists of systems for measuring metabolic flows and valve activity, which can be used on bivalve molluscs for as long as an individual animal's characteristics (e.g. size) make this technically feasible. In this paper, we present some of these non‐invasive techniques with applications for pearl oyster and list other potentially promising techniques. We also focus on a unique method we developed specifically for to record the pearl rotation characteristics within pearl oysters. This article presents the state of the art in non‐invasive functional exploration techniques. We hope that the information provided here will be useful to physiologists of bivalve marine molluscs through the tools and applications presented here or other future approaches based on them.