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This work aimed to study the variability in flowering of five populations of Eucalyptus cladocalyx established in the administrative region of Coquimbo, northern Chile. Flowering was recorded as a binary response trait in 30-month-old trees. Then, at first, a generalized linear model was fitted for analyzing provenance effect. Subsequently, genetic variability was studied within the best provenance by Bayesian inference via Gibbs sampling. Initially, two sites were considered: Caracas and Tunga Norte, in the littoral and interior area of the Choapa Province, respectively. In the littoral area, only 1.3% of the trees evidenced flowering events, while in Tunga Norte, this value was 23.43%. For this reason, only interior site was considered. The provenance effect was significant (p < 0.01), with Cowell (codified FDI-20411) being the population that evidenced a relative better flowering response, although it not was different of the trees from national plantations (FDI-Illapel). However, trees from a local population evidenced a high variability, having a mean response similar to other provenances. The flowering trait analyzed within the Cowell population, the selected provenance, was shown to be highly heritable (h(2) = 52.3%). Predicted genetic gain when considering two different breeding strategies varied from 36 to 40%. According to these results, it is possible that farmers can recover establishment costs of E. cladocalyx plantations as soon as possible whenever the selected trees are used for apicultural aims.