The Bird’s Head Isthmus connecting the Bird’s Head Peninsula with the rest of New Guinea is one of the last pristine areas remaining in Southeast Asia. Dominantly covered by limestone karsts, this vast region of West Papua (Indonesia) is still a terra incognita. At the heart of the coral triangle, the Kumawa and Lengguru limestone karsts and reef slopes are today a major biodiversity reservoir with high levels of endemism. The French-Indonesian ‘Lengguru 2014’ expedition was headed by IRD and P2O-LIPI, RCB-LIPI and POLTEK. Exploration and sampling effort were concentrated on several reef slopes from -100 m to the surface using closed-circuit rebreathers (eCCR) and open circuits. ‘Lengguru 2014’ expedition was the first French oceanographic campaign organized by a national and academic research organization to use the rebreather. The scientific diving operations were made under the responsibility of the French research institute IRD. Nevertheless, the French regulation presently only allows the use of rebreather for recreational uses. The main author participates as an expert for the Ministry of Labor to reform the law with specific applications to scientific purposes. This scientific expedition was therefore permitted in phase advance. The Lengguru 2014 expedition was organized in complete autonomy for 6 weeks. It required extensive preparation and logistics, as well as some strengthened safety procedures for scientific dives. Forty vertical transects have been performed from -100 meters depth to the surface, silently with great autonomy and optimized decompression. The exploration of flooded karsts by cave diving has been also possible with rebreather. It does not bubble and offers such autonomy. The use of eCCR offers together scientific benefits and enhanced diving safety. The ‘Lengguru 2014’ Expedition provided a science-based assessment of functional, genetic and morphological diversity for several marine biotas (echinoderms, hard corals, gorgonians, mollusks) with prime importance for biodiversity conservation.