Hypoxia affects thousands of km2 of marine waters all over the world, and has caused mass mortality of marine animals, benthic defaunation and decline in fisheries production in many places. The severity, frequency occurrence and spatial scale of hypoxia have increased in the last few decades. Due to rapid human population growth and global warming, the problem of hypoxia is likely to become worse in the coming years. Molecular responses of marine animals to hypoxia are poorly known. In many animals, a haem protein probably serves as the cellular sensor for oxygen, and reactive oxygen species are generated as signaling molecules. In mammal and fish, a heterodimeric transcription factor, hypoxia-inducible factor 1 (HIF-1) has been identified. HIF-1 receives signals from the molecular oxygen senor through redox reactions and/or phosphorylation, and in turn, regulates the transcription of a number of hypoxia-inducible genes, including genes involved in erythropoiesis, angiogenesis and glycolysis. These molecular responses then cascade into a series of biochemical and physiological adjustments, enabling the animal to survive better under hypoxic conditions. Marine animals respond to hypoxia by first attempting to maintain oxygen delivery (e.g. increases in respiration rate, number of red blood cells, or oxygen binding capacity of hemoglobin), then by conserving energy (e.g. metabolic depression, down regulation of protein synthesis and down regulation/modification of certain regulatory enzymes). Upon exposure to prolonged hypoxia, animals must eventually resort to anaerobic respiration. Hypoxia reduces growth and feeding, which may eventually affect individual fitness. Effects of hypoxia on reproduction and development of marine animals, albeit important in affecting species survival, remain almost unknown. Many fish and marine organisms can detect, and actively avoid hypoxia. Some benthos may leave their burrows and move to sediment surface during hypoxia. These behaviorial changes may render the animals more vulnerable to predation. Hypoxia may eliminate sensitive species, thereby causing major changes in species composition of benthic, fish and phytoplankton communities. Decreases in species diversity and species richness are well documented, and changes in trophodynamics and functional groups have also been reported. Under hypoxic conditions, there is a general tendency for suspended feeders to be replaced by deposit feeders; demersal fish by pelagic fish; and macrobenthos by meiobenthos. Microflagellates and nanoplankton also tend to dominate in the phytoplankton community in hypoxic environments. Existing evidence suggest that recovery of benthic communities in temperate region take two to several years. Recovery however, appears to be much quicker in subtropical environments. In natural conditions, hypoxia is often associated with increases in ammonia, hydrogen sulphide and particulate organic materials. The inability to isolate effects of hypoxia from interactions of these compounding factors makes it difficult to attribute many of the observed ecological effects to hypoxia.