The main goal of the present research is to classify images of plants to species with deep learning. We used convolutional neural network architectures for feature learning and fully connected layers with logsoftmax output for classification. Pretrained models on ImageNet were used, and transfer learning was applied. In the current research image sets published in the scope of the PlantCLEF 2015 challenge were used. The proposed system surpasses the results of all top competitors of the challenge by 8% and 7% at observation and image levels, respectively. Our secondary goal was to satisfy the users’ needs in content-based image retrieval to give relevant hits during species search task. We optimized the length of the returned lists in order to maximize MAP (Mean Average Precision), which is critical to the performance of image retrieval. Thus, we achieved more than 50% improvement of MAP in the test set compared to the baseline.