The invention provides a transgene identification method and device. The identification method includes: obtaining the to-be-tested data of a sample to be identified, a vector sequence of the sample to be identified, and a host genome sequence; performing a homology alignment between the host genome sequence and the vector sequence of the sample to be identified, and marking, on the vector sequence of the sample to be identified, a region homologous to the host genomic sequence to obtain a marked region; aligning the to-be-tested data with the vector sequence of the sample to be identified toobtain multiple candidate exogenous DNA fragments; removing fragments containing the marked region from the plurality of the candidate exogenous DNA fragments to obtain an exogenous DNA fragment. Themethod marks the homology region on the vector sequence of the sample to be identified in order to remove the marked region from the multiple candidate exogenous DNA fragments obtained by alignment, thereby eliminating false positive errors. Therefore, the identification method is simple and highly accurate.