Chlorophyll fluorescence (CF) is one tool used by researchers to quantify plant water status during periods of limited water availability. The research reported herein was designed to evaluate a CF-based protocol as a tool for use in cotton, Gossypium spp. breeding programs for the identification of drought tolerant genotypes. Twenty genotypes were selected to represent diverse and distinct US germplasm pools. Replicated tests were performed in Lubbock and College Station, TX in 2006 and 2007. Dryland and irrigated treatments, as main plots, were applied in a randomized complete block design, split to genotypes. CF measurements were taken at mid-bloom and late bloom growth stages. Source leaf tissue was harvested at predawn and subjected to high temperature incubation with CF measurements subsequently taken hourly for 5 h. Drought stressed plants had not mobilized their carbohydrate reserves from their source leaves overnight and thus maintained cell viability and therefore higher CF values throughout the incubation and measurement period with the opposite being true for non-stressed plants. Fiber lint yield and fiber properties were measured for comparison with the CF data. Genotype × treatment effects complicated the classification of genotypic response to drought. Few and inconsistent correlations were found among CF values and lint yield or fiber properties. Data suggested that this procedure provides little potential in selecting plants for drought tolerance when plants are grown under field culture.