Complexes of microcystins (MCs) and metal ions were detected with mass spectrometry. To observe the MCs–metals complexes, CryoSpray ionization ion source was developed and it was equipped on a commercial Fourier transform ion resonance mass spectrometer. Mixtures of two MCs and five metals were applied to Fourier transform ion cyclotron resonance mass spectrometry coupled with CryoSpray. The analyses showed complexes of MC-LR–Fe(II), –Zn, –Cu, –Mg, MC-RR–Fe(II), –Zn, –Cu, and –Mg but MC-LR–Fe(III) and MC-RR–Fe(III) were not observed. Present study suggested that MCs may play roles in metal ion uptake and/or accumulation in the algal cells.