In the language of mathematical chemistry, Fibonacci cubes can be defined as the resonance graphs of fibonacenes. Lucas cubes form a symmetrization of Fibonacci cubes and appear as resonance graphs of cyclic polyphenantrenes. In this paper it is proved that the Wiener index of Fibonacci cubes can be written as the sum of products of four Fibonacci numbers which in turn yields a closed formula for the Wiener index of Fibonacci cubes. Asymptotic behavior of the average distance of Fibonacci cubes is obtained. The generating function of the sequence of ordered Hosoya polynomials of Fibonacci cubes is also deduced. Along the way, parallel results for Lucas cubes are given.