Tintinnid ciliates are planktonic grazers of nanoplankton. They have a lorica (or shell) into which the ciliate cell can withdraw. The lorica provides information on both the identity and the ecology of the organism because characteristics of the lorica distinguish species and the diameter of the oral opening is related to the size of prey ingested. We examined the relationship between biodiversity estimates based on classifying specimens as belonging to a species or a simple morphological group defined by lorica oral diameter (LOD) in a presumably species-rich area, a tropical lagoon. Two sites were sampled in the lagoon off Nouméa over an annual cycle. The tintinnid fauna was species-rich (76 species) and represented a relatively even distribution of LOD sizes compared to other sites both tropical and temperate. Median LOD varied with the fraction of the chlorophyll concentration > 10 µm. Total chlorophyll concentration was related to tintinnid concentration and in turn weakly correlated with numbers of species and LOD size-classes. Numbers of species were closely related to numbers of LOD size-classes as were H' of species and H' (Shannon index) of LOD size-classes. Thus, metrics of a morphological characteristic, related to the ecology of the organisms can be used to estimate species diversity.