Three-dimensional (3-D) wake transitions of a steady flow past two side-by-side circular cylinders are investigated through Floquet analysis and direct numerical simulations (DNS) over the gap-to-diameter ratio
$g^*$
up to 3.5 and Reynolds number
${\textit {Re}}$
up to 400. When the flows behind two cylinders form in-phase and anti-phase wakes at large
$g^*$
, the wake transition is similar to the isolated cylinder counterpart, with the critical
${\textit {Re}}$
for the onset of 3-D transition (
${\textit {Re}}_{cr-1}$
) happens at around 180. At small
$g^*$
, 3-D transition becomes interestingly complex due to the distinct characteristics formed in base flows. The
${\textit {Re}}_{cr-1}$
suddenly drops to around 60–100 and forms distinct variation trends with
$g^*$
. Precisely, the
${\textit {Re}}_{cr-1}$
of the single symmetric wake (SS,
$g^*\lessapprox 0.25$
) is more than half of the isolated cylinder counterpart due to the large length scale of the SS wake. Only mode A is detected in SS. In the asymmetric single wake (ASS,
$g^* \approx 0.25\unicode{x2013}0.6$
) and flip-flop wake (FF,
$g^* \approx 0.6\unicode{x2013}1.8$
), the 3-D transition develops at
${\textit {Re}} \approx 103\unicode{x2013}60$
and 75–60, respectively. The decrease in
${\textit {Re}}_{cr-1}$
with increasing
$g^*$
is because of the increased level of wake asymmetry in ASS and irregular vortex shedding in FF. Floquet analysis predicts two new unstable modes, namely mode A
$'$
and subharmonic mode C
$'$
, of ASS. Both modes are transient features in 3-D DNS and the flow eventually saturates into a new 3-D mode, mode ASS. The gap flow of mode ASS is distinctly characterised by its time-independent spanwise waviness structure that is deflected towards different transverse directions with a long wavelength of about
$14$
cylinder diameters. The 3-D mode of the FF is irregular both temporally and spatially. Variations of
${\textit {Re}}_{cr-1}$
with
$g^*$
, the characteristics and the physical mechanisms of each 3-D mode are discussed in this study.