Secondary instability in the flow past two square cylinders in side-by-side arrangements is numerically studied by using a Floquet analysis. The distance between the neighboring faces of the two cylinders (G) is the key parameter which affects the secondary instability under consideration. In this paper, we present the critical Reynolds number for the secondary instability and the corresponding spanwise wave number of the most unstable (or least stable) wave for each G. Our results would shed light on a complete understanding of the onset of secondary instability in the presence of two side-by-side square cylinders.