Conservation practices from the perspective of functional diversity (FD) and conservation prioritization need to account for the impacts of exotic species in freshwater ecosystems. This work first simulated the influence of exotic species on the values of FD in a schemed mechanistic model, and then a practical case study of conservation prioritization was performed in the Min River, the largest river in southeastern China, to discuss whether including exotic species alters prioritization. The mechanistic model revealed that exotic species significantly altered the expected FD if the number of exotic species occupied 2% of the community. Joint species distribution modelling indicated that the highest FD occurred in the west, northwest and north upstreams of the Min River. Values of FD in 64.69% of the basin decreased after the exotic species were removed from calculation. Conservation prioritization with the Zonation software proved that if first the habitats of exotic species were removed during prioritization, 62.75% of the highest prioritized areas were shifted, average species representation of the endemic species was improved and mean conservation efficiency was increased by 7.53%. Existence of exotic species will significantly alter the metrics of biodiversity and the solution for conservation prioritization, and negatively weighting exotic species in the scope of conservation prioritization is suggested to better protect endemic species. This work advocates a thorough estimate of the impacts of exotic species on FD and conservation prioritization, providing complementary evidence for conservation biology and valuable implications for local freshwater fish conservation. 摘要 从功能多样性 (FD)角度的生物多样性保护需要考虑淡水生态系统中外来物种的影响。本研究首先在预设的机械模型中模拟了外来物种对FD值的影响，然后以中国东南部最大的河流，即闽江为例，讨论了引入外来物种是否会改变鱼类多样性保护的优先级顺序。机械模型表明，如果外来物种的数量占群落的2%，则外来物种将显著改变FD的期望值。联合物种分布模型对鱼类物种的分布模拟表明，最高的FD值出现在闽江的西部、西北部和北部上游。剔除外来物种后，64.69%的流域中FD的值下降。Zonation优先级排序的结果表明，如果在优先排序过程中首先移除外来物种的栖息地，62.75%的最高优先级区域被转移，对本地物种的平均保护效率提高了7.53%，本地物种得到了更好的保护。外来物种的存在将显著改变生物多样性的衡量标准和保护优先级的排序结果；多样性保护优先级排序过程中优先剔除外来物种的核心栖息地，可以更好地保护本地物种。本研究建议在多样性保护工作中需完整评估对外来物种对FD的影响，并确定外来物种对保护优先级排序的影响，为本地淡水鱼类的保护提供补了有价值的信息。