Radio Frequency IDentification (RFID) technology has been widely used in missing tag identification to reduce the economic loss caused by theft. Although many advanced works have been proposed, they cannot work properly in an open RFID system with unexpected tags. That is because the unexpected tags may reply to the reader when it is the missing tags’ turn, such that the replies are mistakenly treated as the missing tags’, leading to failure to detect the missing tags. To solve the problem, this article proposes an order-based missing tag identification protocol (OMTI) that efficiently identifies all missing tags even with the presence of unexpected tags. The key of OMTI is that we dynamically assign each tag an exclusive slot rather than use random hashes in traditional design. Namely, OMTI off-line serializes all known tags in advance by assigning each of them a unique and continuous slot, on-line identifies missing tags by checking tags’ responses in each slot, and dynamically updates the slot assignment to ensure the high efficiency of the next execution. Besides, we enhance OMTI to make it embrace newly added tags and spread to the multi-reader case from the single one. The simulation results demonstrate that OMTI can significantly reduce the identification time compared to the state-of-the-art.