The identification of seeds from native species is a complex assessment due to the high Brazilian biodiversity and varied characteristics between species. The objective was to apply different machine learning classifiers associated with image analysis to identify seeds of forest species. In total, 155 native species belonging to 42 botanical families were analyzed. In addition, to determine the appropriate machine learning classifier, five supervised learning classification techniques were implemented: decision trees (DT), artificial neural networks (ANN), k-nearest neighbors (k-NN), Naive-Bayes classifier (NBC) and support vector machine (SVM), which had their performance evaluated. For modeling, 66% of the seeds’ morphobiometric data were used to train the classifiers, while 34% were reserved for validation. The classifiers are promising tools for identifying species from seed images. The decision tree (DT) classifier showed greater accuracy for correct species identification (82.8%), followed by ANN (81.7%), k-NN (81.7%), NBC (81.1%) and SVM (78.7%). Therefore, it is possible to identify seeds of native species from images and machine learning with a satisfactory accuracy rate. Finally, the decision tree classifier is recommended.