Fusion of multiple instances within a modality for biometric verification performance improvement has received considerable attention. In this letter, we present an iris recognition method based on multi-instance fusion, which combines the left and right irises of an individual at the matching score level. When fusing, a novel fusion strategy using minimax probability machine (MPM) is applied to generate a fused score for the final decision. The experimental results on CASIA and UBIRIS databases show that the proposed method can bring obvious performance improvement compared with the single-instance method. The comparison among different fusion strategies demonstrates the superiority of the fusion strategy based on MPM.