For an undirected $n$-vertex graph $G$ with non-negative edge-weights, we consider the following type of query: given two vertices $s$ and $t$ in $G$, what is the weight of a minimum $st$-cut in $G$? We solve this problem in preprocessing time $O(n\log^3 n)$ for graphs of bounded genus, giving the first sub-quadratic time algorithm for this class of graphs. Our result also improves by a logarithmic factor a previous algorithm by Borradaile, Sankowski and Wulff-Nilsen (FOCS 2010) that applied only to planar graphs. Our algorithm constructs a Gomory-Hu tree for the given graph, providing a data structure with space $O(n)$ that can answer minimum-cut queries in constant time. The dependence on the genus of the input graph in our preprocessing time is $2^{O(g^2)}$.