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Overlapping in operations is an effective technology for productivity improvement in modern manufacturing systems. Thus far, however, there are still rare works on flexible job shop scheduling problems (FJSPs) concerning this strategy. In this paper, we present a hybrid artificial bee colony (hyABC) algorithm to minimise the total flowtime for a FJSP with overlapping in operations. In the proposed hyABC, a dynamic scheme is introduced to fine-tune the search scope adaptively. In view of poor exploitation ability of artificial bee colony algorithm, a modified migrating birds optimisation algorithm (MMBO) is developed and integrated into the search process for better balancing global exploration and local exploitation. In MMBO, a forward share strategy with one-job based crossover is designed to make good use of valuable information from behind solutions. Besides, an improved downward share scheme is adopted to increase diversification of the population, and thus alleviate the premature convergence. Extensive experiments based on benchmark instances with different scales are carried out and comparisons with other recent algorithms identify the effectiveness of the proposed hyABC.