Given two graphs and and a function , Hedetniemi [9] defined the \emph{function graph} by and . Whenever , the function graph was called a functigraph by Chen, Ferrero, Gera, and Yi [7]. A function graph is a generalization of the -permutation graph introduced by Chartrand and Harary [5]. The independence number of a graph is the size of a largest set of mutually non-adjacent vertices. In this paper, we study independence number in function graphs. In particular, we give a lower bound in terms of the order and the chromatic number, which improves on some elementary results and has a number of interesting corollaries.