High temperature stress is a major limitation to commercial production of habanero pepper (Capsicum chinense Jacq.) in tropical and subtropical regions. The ability to sustain physiological activity under stress is an important trait for newer varieties. We evaluated leaf thermotolerance [based on the cell membrane stability (CMS) test] of three habanero pepper varieties to: 1) determine genetic variability in CMS among the genotypes studied; and 2) to assess correlations between CMS, photosynthesis and chlorophyll fluorescence [(CF), an indicator of membrane-dependent photosystem II quantum efficiency, ΦPSII]. The genotypes evaluated were TAM Mild Habanero (TMH, a recently developed mild habanero pepper) and its closely related parents (Yucatan and PI 543184). Net CO2 assimilation rate (An) of intact leaves was measured in the field and leaf samples collected and exposed to heat stress (55 °C for 20 min) in temperature-controlled water baths under dim light conditions. The CF was assessed before and after the heat treatment. The CMS was highest in PI 543184, lowest in TMH and intermediate in Yucatan. All genotypes maintained high An rates in the field (25 ± 6 μmol·m-2·s-1); however, correlations between An and CMS were weak. The Φ values were similar among the genotypes (∼0.8) under nonstress conditions, but differed significantly following stress exposure. PI 543184 had the highest post-stress ΦPSII values (0.506 ± 0.023), followed by Yucatan (0.442 ± 0.023) and TMH (0.190 ± 0.025). Observed differences in CMS and ΦPSII indicate plasticity in the response to heat stress among these genotypes.