In this paper, we propose a novel method for plant leaves recognition by incorporating an unsupervised convolutional auto-encoder (CAE) and Siamese neural network in a unified framework by considering Siamese as an alternative to the conventional loss of CAE. Rather than the conventional exploitation of CAE and Siamese, in our case we have proposed to extend CAE for a novel supervised scenario by considering it as one-class learning classifier. For each class, CAE is trained to reconstruct its positive and negative examples and Siamese is trained to distinguish the similarity and the dissimilarity of the obtained examples. On the contrary and asymmetric to the related hierarchical classification schemes which require pre-knowledge on the dataset being recognized, we propose a hierarchical classification scheme that doesn’t require such a pre-knowledge and can be employed by non-experts automatically. We cluster the dataset to assemble similar classes together. A test image is first assigned to the nearest cluster, then matched to one class from the classes that fall under the determined cluster using our novel one-class learning classifier. The proposed method has been evaluated on the ImageCLEF2012 dataset. Experimental results have proved the superiority of our method compared to several state-of-the art methods.