Analysis of the structure and fruiting behavior of cotton, Gossypium hirsutum L., is complicated by its indeterminate growth habit and size variation among individual plants. We present COTMAP, a technique in which the primary fruiting sites (first and second sympodial positions) are individually mapped and fruit on remaining sites are considered collectively. Yield variables calculated by COTMAP include total bolls, boll distribution, and boll retention in prime fruiting sites. Plant structure variables include node of first fruiting branch, number of monopodia, number of sympodia, number of effective sympodia, number of sympodia with at least two flowering positions, total number of main axis nodes, plant height, and average internode length. Data from three tests of mepiquat chloride (N,N‐dimethyl‐piperidinium chloride) on cotton are used to illustrate the mapping technique. The COTMAP technique has been used to distinguish variation in structural characteristics and fruiting pattern of cotton plants associated with genetic differences, growth regulators, and insect damage.