Variation in respiratory traits was quantified between two populations of the sailfin molly Poecilia latipinna(one from a periodically hypoxic salt marsh, Cedar Key, and one from a chronically normoxic river site, Santa Fe River). Two suites of characters were selected: traits that may show both short-term acclimation response and interdemic variation in acclimation response (metabolic rate, critical oxygen tension and respiratory behaviour), and those that are not likely to respond to short-term acclimation but may vary among populations (gill morphometric characters). Sailfin mollies from the salt marsh, acclimated to hypoxia (1 mg l−1, c. 20 mmHg) for 6 weeks, spent less time conducting aquatic surface respiration and had lower gill ventilation rates than hypoxia-acclimated conspecifics from the well-oxygenated river site. Poecilia latipinna acclimated to hypoxia exhibited a lower critical oxygen tension (Pc) than fish acclimated to normoxia; however, there was also a significant population effect. Poecilia latipinna from Cedar Key exhibited a lower Pc than fish from the Santa Fe River, regardless of acclimation. Cedar Key fish had a 14% higher mean gill surface area relative to fish from the Santa Fe River, a character that could account, at least in part, for their greater tolerance to hypoxia.