We consider nonparametric estimation of the transition operator $P$ of a Markov chain and its transition density $p$ where the singular values of $P$ are assumed to decay exponentially fast. This is for instance the case for periodised, reversible multi-dimensional diffusion processes observed in low frequency. We investigate the performance of a spectral hard thresholded Galerkin-type estimator for $P$ and ${p}$, discarding most of the estimated singular triplets. The construction is based on smooth basis functions such as wavelets or B-splines. We show its statistical optimality by establishing matching minimax upper and lower bounds in $L^2$-loss. Particularly, the effect of the dimensionality $d$ of the state space on the nonparametric rate improves from $2d$ to $d$ compared to the case without singular value decay.