This paper presents a novel approach for accurate counting and localization of tropical plants in aerial images that is able to work in new visual domains in which the available data is not labeled. Our approach uses deep learning and domain adaptation, designed to handle domain shift between the training and test data, which is a common challenge in this agricultural applications. This method uses a source dataset with annotated plants and a target dataset without annotations, and adapts a model trained on the source dataset to the target dataset using unsupervised domain alignment and pseudolabeling. The experimental results show the effectiveness of this approach for plant counting in aerial images of pineapples under significative domain shift, achieving a reduction up to 97% in the counting error when compared to the supervised baseline.