This study analyzed the transcriptome responses of cotton (Gossypium hirsutum) during compatible and incompatible interactions with the root-knot nematode (Meloidogyne incognita). RNA sequencing was performed on samples from a susceptible and a resistant cotton line over multiple time points during infection. During the incompatible interaction, twice as many genes were differentially expressed compared to the compatible interaction. Defense-related genes were often downregulated during early compatible interaction but induced earlier and to a higher degree during incompatible interaction. A number of differentially expressed genes located within known root-knot nematode resistance quantitative trait loci were identified as potential resistance candidates. The results provide insights into the molecular basis of resistance in cotton to root-