The use of oversampling at the receiver results in colored noise when the bandwidth of the noise-limiting filter is not sufficiently large. This paper proposes a fractionally-spaced single-carrier linear MMSE frequency domain equalizer (LMMSE-FDE) over frequency-selective multiple input multiple output (MIMO) channels. The performance of the fractionally-spaced LMMSE-FDE with colored noise samples is analyzed and the relation between the time domain correlation and the frequency domain correlation of noise samples is presented. Simulation results show that the proposed technique significantly outperforms the conventional frequency domain equalization by exploiting the frequency domain correlation of noise samples.