Classical sampling methods often miss important components of coral reef biodiversity, notably organisms that remain sheltered within the coral matrix. Recent studies using sea kraits (sea snakes) as bio-indicators suggest that the guild of predators represented by anguilliform fish (Congridae, Muraenidae, Ophichthidae, henceforth “eels” for simplicity) were far more abundant and diverse than previously suspected. In the current study, eel diversity (similarity and species richness indices) estimated via sea snake sampling (SSS) was compared among six areas of one of the main oceanic biodiversity hotspot of the Pacific Ocean (southwest lagoon of New Caledonia). Based on the eel diversity in the snakes’ diet, the results obtained in six areas, in two snake species, and using different estimates (ANOSIM, Shannon index…) were consistent, suggesting that SSS provided robust information. Analyses also suggested subtle, albeit significant, differences in the eel assemblages among islets. Such spatial differences are discussed in light of local management practices. As SSS is easy to use, cost-effective, and provides the best picture of eel assemblages to date, it can be employed to monitor the eel assemblages in addition to the snakes themselves in many areas of the Indo-Pacific Ocean, thereby providing an index of the top predator biodiversity of many coral reefs.