This is the first study to investigate the rate of mercury (Hg) biomagnification in the aquaculture pond ecosystem of the Pearl River Delta (PRD), China, by analyzing total mercury (THg) and methyl mercury (MeHg) concentrations in various species of fish at different trophic levels (TLs). Species representing a gradient of trophic positions in the aquaculture pond food chains were chosen for analyzing THg and MeHg concentrations. In this study, there were two kinds of the aquaculture pond food chains: (1) omnivorous (fish feeds, zooplankton, grass carp [Ctenopharyngodon idellus], and bighead carp [Aristichthys nobilis]) and (2) predatory (zooplankton, mud carp [Cirrhina molitorella], and mandarin fish [Siniperca kneri]). Bighead carp and mandarin fish had the highest MeHg and THg concentrations, i.e., an order of magnitude higher than other species, in their respective food chains. More than 90% of the THg concentrations detected in bighead carp, mandarin fish, and mud carp were in the methylated form. In this study, %MeHg increased with TLs and MeHg concentrations, reflecting that MeHg is the dominant chemical species of Hg accumulated in higher concentrations in biota, especially biota associated with higher TLs in the food chains. The trophic magnification factors were 2.32 and 2.60 for MeHg and 1.94 and 2.03 for THg in omnivorous and predatory food chains, respectively, in PRD. Hg concentrations in fish tissue correlated to Hg levels in the ambient environment, and sediment seemed to be the major source for Hg accumulated in fish. In addition, feeding habit also affected Hg accumulation in different fish species. Four significant linear relationships were obtained between log-THg and δ15N and between log-MeHg and δ15N. The slope of the regression equations, as biomagnification power, was smaller in magnitude compared with those reported for temperate and arctic marine and freshwater ecosystems, indicating that THg and MeHg biomagnifications were lower in this PRD subtropical aquaculture pond ecosystem. This was probably due to low Hg bioavailability at lower TLs as well as individual feeding behavior of fish.