We studied the breeding systems of four populations of Enterolobium cyclocarpum (guanacaste, earpod tree) in Costa Rica. Multilocus estimates of the outcrossing rate indicate that E. cyclocarpum is a predominant outcrossing species (tm ranged between 0.881 and 0.901) and biparental inbreeding is low (range between 0.058 and 0.079). Overall, our analyses showed significant differences in the gene frequencies between pollen and ovules and significant differences in pollen gene frequencies between the four populations. We also found significant differences in the pollen gene frequencies calculated for single trees in the same population. Outcrossing rates and pollen gene frequencies varied in two consecutive years in two populations of E. cyclocarpum. The correlated mating model revealed that there are differences in the correlation of paternity between populations and years. These findings indicate that there is variation in the average number of trees that father the seed crop of each tree and/or that some fathers are overrepresented in the seed crop of each tree. The implication of these findings for the development of strategies for conservation and management of this species are discussed.