Deep learning has become essential in the biological species recognition task. However, a significant challenge is the ability to continuously learn new or mutated species with limited annotated samples. Since species within the same family typically share similar traits, distinguishing between new and existing (old) species during incremental learning often faces the issue of species confusion. This can result in "catastrophic forgetting" of old species and poor learning of new ones. To address this issue, we propose a Prototype Antithesis (PA) method, which leverages the hierarchical structures in biological taxa to reduce confusion between new and old species. PA operates in two steps: Residual Prototype Learning (RPL) and Residual Prototype Mixing (RPM). RPL enables the model to learn unique prototypes for each species alongside residual prototypes representing shared traits within families. RPM generates synthetic samples by blending features of new species with residual prototypes of old species, encouraging the model to focus on species-unique traits and minimize species confusion. By integrating RPL and RPM, the proposed PA method mitigates "catastrophic forgetting" while improving generalization to new species. Extensive experiments on CUB200, PlantVillage, and Tree-of-Life datasets demonstrate that PA significantly reduces inter-species confusion and achieves state-of-the-art performance, highlighting its potential for deep learning in biological data analysis.