Objective. This study introduces and evaluates a novel target identification method, latent common source extraction (LCSE), that uses subject-specific training data for the enhancement of detection of steady-state visual evoked potential (SSVEP). Approach. LCSE seeks to construct a common latent representation of the SSVEP signal subspace that is stable across multiple trials of electroencephalographic (EEG) data. The spatial filter thus obtained improves the signal-to-noise ratio (SNR) of the SSVEP components by removing nuisance signals that are irrelevant to the generalized signal representation learnt from the given data. In this study a comparison of SSVEP identification performance between the proposed method, extended canonical correlation analysis (ExtCCA) and multiset canonical correlation analysis (MsetCCA) was conducted using SSVEP benchmark data of 40 targets recorded from 35 subjects to validate the effectiveness of the LCSE framework. Main results. The results indicate that the LCSE framework significantly outperforms the other two methods in terms of both classification accuracy and information transfer rates (ITRs). Significance. The significant improvement in the target identification performance demonstrates that the proposed LCSE method can be seen as a promising potential candidate for efficient SSVEP detection in brain-computer interface (BCI) systems. © 2019 IOP Publishing Ltd.