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Mangroves are valuable contributors to coastal ecosystems; knowledge of the dynamics of mangrove ecosystems is important in the context of global change. To obtain this knowledge, remote sensing is an indispensable means, yet it poses challenges since the accuracy is sometimes unsatisfactory in distinguishing mangroves from other land cover types with traditional classification methods. In this letter, we proposed a modified artificial immune algorithm (AIA), in which the antibodies represent the candidate solutions and the antigens are expressed by the fitness function. Multiclass coevolution was combined with the concept of clonal selection to ensure computation of an optimal clustering center in parallel for each land cover type. A cluster-center-oriented decimal encoding method for antibodies was adopted, and the inner class variance and the between-class difference together were used to formulate the fitness function. Furthermore, a design of the antibody solubility-based selection operator and nonuniform mutation operator was undertaken. Applying this modified AIA to a Landsat Thematic Mapper multispectral remote sensing imagery in the Zhangjiang estuary in southeastern China, we found that the AIA substantially improved classification accuracy over traditional methods, showing an overall accuracy of 90% (kappa coefficient = 0.88) and was capable to discern mangrove well (commission of 10% and omission of 22%).