We present the analysis of 4 months of Kepler photometry of the K4V star HAT-P-11 , including 26 transits of its “ super-Neptune ” planet . The transit data exhibit numerous anomalies that we interpret as passages of the planet over dark starspots . These spot-crossing anomalies preferentially occur at two specific phases of the transit . These phases can be understood as the intersection points between the transit chord and the active latitudes of the host star , where starspots are most abundant . Based on the measured characteristics of spot-crossing anomalies , and previous observations of the Rossiter-McLaughlin effect , we find two solutions for the stellar obliquity \psi and active latitude l : either \psi = 106 ^ { +15 } _ { -11 } and l = 19.7 ^ { +1.5 } _ { -2.2 } , or \psi = 97 ^ { +8 } _ { -4 } and l = 67 ^ { +2 } _ { -4 } ( all in degrees ) . If the active latitude changes with time in analogy with the “ butterfly diagram ” of the Sun ’ s activity cycle , future observations should reveal changes in the preferred phases of spot-crossing anomalies .