Alertness seems to influence selective attention processes underlying cognitive control in the flanker task, as indicated by previous findings of larger congruency effects on alert trials (in which task stimuli are preceded by alerting cues) than on no-alert trials. One hypothesis for the alerting-congruency interaction is that increased alertness promotes spatial grouping of the target and distractors. In the present study, the author tested the spatial grouping hypothesis in three experiments in which the spatial alignment (collinearity) of the target and distractors was manipulated. Reliable alerting-congruency interactions were obtained, and congruency effects on response times were smaller for misaligned stimuli than for aligned stimuli in all experiments. However, the alerting-congruency interactions were not consistently modulated by alignment, contrary to a prediction derived from the spatial grouping hypothesis. The results suggest that spatial grouping is not a viable mechanism for explaining the alerting-congruency interaction in the flanker task, helping to prune the space of theoretical possibilities for linking alertness to cognitive control.