ARIA is an ARM repeat protein that is a positive regulator of ABA response. To identify ARIA-interacting proteins, we conducted yeast two-hybrid screening. One of the positive clones obtained from the screen encoded a protein kinase, AtNEK6, which belongs to the NIMA (Never In Mitosis, gene A)-related kinase family. We analyzed AtNEK6 overexpression (OX) and knockout (KO) lines to investigate its in vivo function. The AtNEK6 OX lines grew slowly, whereas the KO line germinated and grew faster than wild type plants. AtNEK6 also affected ABA and stress responses. During seed germination, AtNEK6 OX lines were hypersensitive to ABA and high osmolarity, whereas its KO line was partially insensitive to ABA and high osmolarity. Previously, AtNEK6 was shown to be involved in epidermal cell morphogenesis. Our results indicate that AtNEK6 is also involved in plant growth regulation and responses to ABA and high osmolarity during the seed germination stage.