Plant domestication depends on human perception of intraspecific variation and operates through management practices. Aguirre-Dugua et al. examine the recognition of varieties (one wild, three domesticated) of the gourd (calabash) tree Crescentia cujete by Maya people in Mexico in relation to fruit morphology and ongoing processes of human selection. The results show that Maya nomenclature is related to a preference for domesticated varieties with larger, rounder and thicker fruits. Vegetative propagation of preferred varieties has maintained a differential distribution of cpDNA haplotypes in villages as compared to sympatric wild populations, although tolerance of spontaneous trees favours introgression from wild populations.