Two independent spheres were placed in a side by side arrangement and flow structure in the wake region of the spheres was investigated with a Particle Image Velocimetry (PIV) system when the spheres were in a boundary layer over a flat plate as a special case. Reynolds number was 5000 based on the sphere diameter which was 42.5 mm. Boundary layer was tripped 8mm away from the leading edge of the flat plate with a 5 mm trip wire. The thickness of the hydrodynamically developed boundary layer was determined as 63mm which was larger than the sphere diameter of D=42.5mm. Wake region of the spheres was examined from point of flow physics for the different sphere locations in the ranges of 0≤G/D ≤1.5 and 0≤S/D ≤1.5 where G and S were the distance between the spheres and the distance between the bottom point of the spheres and the flat plate surface, respectively. Depending on the different sphere locations, instantaneous and time averaged vorticity data, scalar values of time-averaged velocity components and their root mean square (rms) values and time averaged vorticity data are presented in the study for the evaluation of wake region of the spheres. It is demonstrated that the gap between the two spheres and the interaction between the gap and the boundary layer greatly affects flow pattern, especially when spheres are located near to the flat plate surface, i.e. S/D=0.1 for 0≤G/D ≤1.5. Different distances between the spheres resulted in various flow patterns as the spheres were approached to the flat plate. The distance S/D=0.1 for all gap values has the strongest effect on the wake structures. Beyond G/D=1.0, the sphere wakes tend to be similar to single sphere case. The instantaneous vorticity fields of the side by side arrangements comprised wavy structures in higher level comparing to an individual sphere case. The gap flow intensifies the occurrence of small scale eddies in the wake region. The submersion rate of the spheres actually determines the characteristics of the wake region and is affected from boundary layer flow in a gradually decreasing manner. © 2014 EDP Sciences.