<p><strong>Abstract.</strong> The periodicity of Saturn kilometric radiation (SKR) varies with time, and its two periods during the first 5 years of the Cassini mission have been attributed to SKR from the northern and southern hemisphere. After Saturn equinox in August 2009, there were long intervals of time (March 2010 to February 2011 and September 2011 to June 2012) with similar northern and southern SKR periods and locked SKR phases. However, from March to August 2011 the SKR periods were split up again, and the phases were unlocked. In this time interval, the southern SKR period slowed down by ~ 0.5% on average, and there was a large jump back to a faster period in August 2011. The northern SKR period speeded up and coalesced again with the southern period in September 2011. We argue that this unusual behavior could be related to the so-called Great White Spot (GWS), a giant thunderstorm that raged in Saturn's atmosphere around that time. For several months in 2011, the visible head of the GWS had the same period of ~ 10.69 h as the main southern SKR modulation signal. The GWS was most likely a source of intense gravity waves that may have caused a global change in Saturn's thermospheric winds via energy and momentum deposition. This would support the theory that Saturn's magnetospheric periodicities are driven by the upper atmosphere. Since the GWS with simultaneous SKR periodicity measurements have only been made once, it is difficult to prove a physical connection between these two phenomena, but we provide plausible mechanisms by which the GWS might modify the SKR periods.</p>