We present a quasi-linear algorithm to compute isogenies between Jacobians of curves of genus 2 and 3 starting from the equation of the curve and a maximal isotropic subgroup of the l-torsion, for l an odd prime number, generalizing the Vélu's formula of genus 1. This work is based from the paper Computing functions on Jacobians and their quotients of Jean-Marc Couveignes and Tony Ezome. We improve their genus 2 case algorithm, generalize it for genus 3 hyperelliptic curves and introduce a way to deal with the genus 3 non-hyperelliptic case, using algebraic theta functions.