AbstractFollowing van der Poorten, we consider a family of nonlinear maps that are generated from the continued fraction expansion of a function on a hyperelliptic curve of genus g. Using the connection with the classical theory of J‐fractions and orthogonal polynomials, we show that in the simplest case g = 1 this provides a straightforward derivation of Hankel determinant formulae for the terms of a general Somos‐4 sequence, which were found in a particular form by Chang, Hu, and Xin. We extend these formulae to the higher genus case, and prove that generic Hankel determinants in genus 2 satisfy a Somos‐8 relation. Moreover, for all g we show that the iteration for the continued fraction expansion is equivalent to a discrete Lax pair with a natural Poisson structure, and the associated nonlinear map is a discrete integrable system. © 2020 the Authors. Communications on Pure and Applied Mathematics is published by Wiley Periodicals LLC.