Other indicator species used by the BINU to assess status of marine and coastal biodiversity include records of whalesharks, humpback whales and Irrawaddy dolphins. There are, however, insufficient data available for assessment.

The whale shark, Rhincodon typus, is one of two protected species in the Philippines and is listed as vulnerable in the IUCN Red List Criteria and Appendix II of Convention on International Trade on Endangered Species (CITES). Whale sharks (and manta rays) are also protected by DA-FAO 193, S. 1998 which bans the “taking or catching, selling, purchasing and possession, transporting and exporting of whale sharks and manta rays”.  There is no study on population estimates on any species of sharks in the Philippines. Anectodal claims of population in Donsol, Sorsogon in the 1990s was between 50 to 100 individuals. A decline in sighting rate was documented in Donsol between 1998 and 1999 using tourist-based sighting data (Grover 2000, Alava and Yaptinchay 2000 as cited in BFAR-NFRDI-PAWB, 2005). The World Wildlife Fund (WWF) -Philippines has initiated participatory research to identify individuals of the whale shark population in Donsol through distinguishing marks, sex, behaviour and photo-documentation. Whale shark aggregation sites have also been identified as priority conservation areas.

At present, the DA-BFAR is finalizing the National Plan of Action (NPOA) for the conservation and management of sharks in the Philippines. The main objective of the NPOA-Shark is to ensure conservation and management of sharks (all chondrichthyan or cartilaginous fishes, comprising the true sharks, winged sharks (skates and rays, also referred to as batoids), and silversharks (or chimaeras), and their long-term sustainable use.  The NPOA hopes to provide a national guideline for managers and interested stakeholders on how to incorporate the conservation and management issues concerning sharks and rays into the overall management of fisheries resources (DA-BFAR, 2008).

Humpback whales have been observed off Babuyan Islands located at the northernmost tip of Luzon. Babuyan Islands is a significant marine conservation area, the only known breeding ground for humpback whales that migrate annually to the Philippines to breed. Over 100 individuals have been photo-identified from surveys conducted since 2000 (Acebes, et al. 2007 as cited in CREE website). The area is also being developed as a model ecotourism site for cetacean interaction in partnership with the local governments and other stakeholder groups, and with the assistance of national government agencies and conservation groups such as the World Wildlife Fund-Philippines and the Center for Rural Empowerment and the Environment (CREE). However, conscious efforts are necessary to balance marine resources conservation and ecotourism development, and to build local capacity in order to maximize and sustain the benefits that can be derived from these resources.

Irrawaddy dolphins, Orcaella brevirostris, are found in estuaries and semi-enclosed water bodies such as bays and sounds. They are listed in Appendix 1 of the Convention on Migratory Species (CMS) to which the Philippines is a member-party. Range states of this migratory species are encouraged to develop a conservation and management plan for implementation by other range countries. In the Philippines, there is only one known population of less than 100 found in Malampaya Sound. Major threats to this population include accidental killing in fishing gear, habitat degradation, possibly prey depletion from over-fishing and the destruction of fish spawning grounds (Dolar et al. 2002 as cited in BFAR-NFRDI-PAWB, 2005). Several mortalities have been recorded, averaging about 4 a year. Experts propose to minimize fishing gear-dolphin interaction to avoid mortalities.