Homeobox (Hox) genes control the most basic functions of development, mostly concerned with the bodyplan. HOX genes code for transcription factors, which are proteins that bind to DNA and either promote or suppress the expression of other genes; and it is this fact that immediately answers Wells' question. A horse's Hox genes may be basically identical to a fly's, but the genes affected by those Hox genes are not. Moreover, the similarity of the two organisms' Hox genes would imply that there should be a certain degree of commonality between their physiological layouts at the most basic level such as bilateral symmetry, anterior-posterior differentiation, etc.
Guess what, both flies and horses have a left and a right, a head at one end, an anus at the other, and limbs in between.
There's a nice introduction to Hox By PZ Myers over at Nature (here).