Pairings on the Jacobians of (hyper-)elliptic curves have received considerable attention not only as a tool to attack curve based cryptosystems but also as a building block for constructing cryptographic schemes with new and novel properties. Motivated by the work of Scott, we investigate how to use efficiently computable automorphisms to speed up pairing computations on two families of non-supersingular genus 2 hyperelliptic curves over prime fields. Our findings lead to new variants of Miller’s algorithm in which the length of the main loop can be up to 4 times shorter than that of the original Miller’s algorithm in the best case. We also implement the calculation of the Tate pairing on both a supersingular and a non-supersingular genus 2 curve with the same embedding degree of $k = 4$. Combining the new algorithm with known optimization techniques, we show that pairing computations on non-supersingular genus 2 curves over prime fields use up to 55.8% fewer field operations and run about 10% faster than supersingular genus 2 curves for the same security level.