Previous findings that skill learning is associated with the formation and preferential stabilization of new dendritic spines in cortex have raised the possibility that this preferential stabilization is a mechanism for lasting skill memory. We investigated this possibility in adult mice using in vivo two-photon imaging to monitor spine dynamics on superficial apical dendrites of layer V pyramidal neurons in motor cortex during manual skill learning. Spine formation increased over the first 3 days of training on a skilled reaching task, followed by increased spine elimination. A greater proportion of spines formed during the first 3 training days were lost if training stopped after 3, compared with 15 days. However, performance gains achieved in 3 training days persisted, indicating that preferential new spine stabilization was non-essential for skill retention. Consistent with a role in ongoing skill refinement, the persistence of spines formed early in training strongly predicted performance improvements. Finally, while we observed no net spine density change on superficial dendrites, the density of spines on deeper apical branches of the same neuronal population was increased regardless of training duration, suggestive of a potential role in the retention of the initial skill memory. Together, these results indicate dendritic subpopulation-dependent variation in spine structural responses to skill learning, which potentially reflect distinct contributions to the refinement and retention of newly acquired motor skills.