The taxonomic status of species in the genus Emydocephalus is uncertain. There are currently two described species, however, it has been suggested that populations of E. annulatus in the Philippines are a distinct species (Alcala et al. 2000). There has, however, been no formal description of a third species of Emydocephalus at this stage. Molecular work is needed to determine the taxonomic status of species in the genus Emydocephalus and the taxonomic affinities of populations in various parts of its range.

Although this species is found over a wide geographic range it only occurs in very discrete populations, has high site fidelity and a highly specialized diet. It is possible that E. annulatus comprises several species, each with a relatively small geographic range.

Populations on Timor Sea reefs have undergone recent population declines, particularly on Ashmore Reef. The reasons for this decline are unknown. The extent of declines on other Timor Sea reefs is unclear as regular detailed surveys have only been conducted at Ashmore Reef.

This species is common in other parts of the range, and although there have been declines in some places, the declines do not reach the thresholds for the threatened categories.This species is listed as Least Concern.

This species, as currently described, is found in the waters of tropical Australia from the Timor Sea to the southwestern Pacific Ocean (Heatwole 1999). It is also found in the Philippines (Alcala et al. 2000) and in New Caledonia and the Loyalty Islands (Ineich and Laboute 2002). It has a highly disjunct distribution throughout its range. For example, in Australia it is found in the Great Barrier Reef (East Coast) and on Timor Sea reefs (West Coast) but not in the Gulf of Carpentaria (North Coast).

This species has a highly aggregated distribution. It can occur  in large numbers, however, it is only found in discrete locations and at a limited number of sites throughout its relatively large geographic range (V. Lukoschek pers. comm. 2009). It also appears to be relatively site attached at the discrete locations where it occurs. For example, this species is very abundant on some Australian reefs in the Timor Sea (Guinea 2006, 2007) and several reefs in the southern Great Barrier Reef (Lukoschek et al. 2007), as well as at certain locations in New Caledonia (Shine et al. 2005), the Loyalty Islands (Rasmussen 2001) and the Philippines (Alcala et al. 2000).

There have been large population declines of this species at Ashmore Reef over the past eight to ten years (M. Guinea pers. comm. 2009). Abundance estimates in the vicinity of the inner mooring at Ashmore Reef in 1994, 1996 and 1998 from mark-recapture surveys were ~100 to 200 individuals (Guinea and Whiting 2005). Sighting rates during the same survey periods were 10 to >25 per hour (Guinea 2006, 2007). Although no subsequent mark-recapture abundance estimates are available, subsequent sighting rates (2001-2005) have dropped to 1-2 per hour for this species at the same location (Guinea 2006, 2007). This reduction in population size is also associated with major declines in abundance of other sea snake species at Ashmore Reef (Guinea 2006, 2007).

This species occurs in association with coral and rocky areas and over sand (Minton and Heatwole 1975, Minton and Dunson 1985). It is generally found in shallow water less than 15 m deep (Minton and Dunson 1985) although it has been seen at a maximum of 40m in the Philippines (Alcala et al. 2000) and elsewhere (V. Lukoschek pers. comm. 2009).

Feeds exclusively on fish eggs and seems to prefer eggs that are laid in nests attached to corals and rocks by species such as damselfish, blennies and gobies (Voris 1966). This is accomplished by scraping the eggs from the substrate with the enlarged scale on each side of the upper lip (Guinea 1996). This species forages over open sand plains at the junction of sand and coral and is typically found close to the benthos and shelters on the bottom edge of corals (Shine et al. 2004, Heatwole 1999).

This species has been noted to have complex social behaviour (Shine et al. 2005). Studies in New Caledonia have found that individuals of this species appear to move about in distinct social groups. Moreover, the species appears to have extremely high site fidelity and estimates of genetic distance between east and west Australian populations (Lukoschek and Keogh 2006) suggest it has very low dispersal potential; thus, it is unlikely to be able to re-establish isolated populations following local extinctions.

This species is very occasionally captured in trawler bycatch but the rarity of this occurrence means that it is not a major threat. For example, no individual of this species has been taken as bycatch in the Queensland trawl fishery, most likely due to the close association of this species with coral reefs where trawlers do not fish (Courtney et al. 2009).

The main threat to this species is likely to be associated with loss or degradation of coral reef habitats, however there is no direct evidence about the nature or extent to which this is the case (Lukoschek et al. 2007). Nonetheless, the highly specialised diet and habitat preference of this species suggests that it will be threatened by all processes resulting in loss of fish species that lay eggs in nests (such as damselfish) as it forages exclusively on fish eggs and tends to prefer fish eggs in demersal nests.

In addition, it has been suggested that increased sea surface temperatures, coral bleaching, and resulting changes in habitat complexity may be linked to localized population declines of sea snakes on Ashmore Reef, northern Australia (Francis 2006) and suggests that climate change may impact sea snake populations (Francis 2006). However, there is little direct evidence about the nature and extent to which the effects of climate change will affect E. annulatus.

There is limited gene flow between populations of this species on the east and west coasts of Australia (Lukoschek and Keogh 2006), suggesting that populations are unlikely to recover from local extinctions by dispersal.

There are no conservation measures specific to this species. Continued monitoring of the status of Ashmore Reef populations is needed and baseline data of population abundances throughout the rest of its range needs to be obtained (V. Lukoschek pers. comm. 2009).

No sea snake species is currently listed by CITES (the Convention on International Trade in Endangered Species of Wild Fauna and Flora).