In the early 1860s the crisis in Kansas prompted Gilpin to join the Republican Party, putting him at odds with many citizens of Missouri. His political alignment with the new administration of U.S. President Abraham Lincoln was rewarded in 1861 when Lincoln appointed him governor of the newly formed Territory of Colorado. His selection over the local favorite William Larimer came as a surprise to many, and was motivated in part by the fact that Gilpin was backed by the Governor of Missouri, a slave state that Lincoln was eager to keep in the Union.