Emu (Dromaius novaehollandiae) has seasonal fat deposition (April - August in North America). Back and abdominal fat of farm emu is rendered into oil, which has good anti-oxidant and anti-inflammatory properties and has been used widely in cosmetics as a carrier. The objective of our research is to identify and study candidate genes that may be useful in marker-assisted selection to improve fat production. The fatty acid binding protein (FABP), stearoyl-CoA desaturase-1 (SCD-1), adiponectin (AdipoQ), adiponectin receptor 1 (AdipoR1), adiponectin receptor 2 (AdipoR2) and leptin receptor (LepR) are key enzymes/hormones involved in fat metabolism and signalling pathway. Full-length cDNA sequences of these genes were isolated from emu back fat using the rapid amplification of cDNA ends (RACE) based on EST sequences. The amino acid sequences of emu FABP and SCD-1 share more similarity with waterfowl (seasonal breeder) than domestic chicken (non-seasonal). Body weights were measured and back fat tissues were collected for gene transcription level in April, June, August and November. Females started fat accumulation sooner and accumulated more fat than males by August. Males started to accumulate fat later than females but by November had significantly more fat than females. Quantitative PCR results indicated that mRNA levels for the genes examined were significantly different from April to November. Expression levels were high for FABP and SCD-1, intermediate for AdipoQ and AdipoR2, and low for AdipoR1 and LepR. Fat weight gain during this period significantly regressed on mRNA levels but the pattern of association was different for the different genes.