We introduce a divergence measure between data distributions based on operators in reproducing kernel Hilbert spaces defined by infinitely divisible kernels. The empirical estimator of the divergence is computed using the eigenvalues of positive definite matrices that are obtained by evaluating the kernel over pairs of samples. The new measure shares similar properties to Jensen-Shannon divergence. Convergence of the proposed estimators follows from concentration results based on the difference between the ordered spectrum of the Gram matrices and the integral operators associated with the population quantities. The proposed measure of divergence avoids the estimation of the probability distribution underlying the data. Numerical experiments involving comparing distributions and applications to sampling unbalanced data for classification show that the proposed divergence can achieve state of the art results.