Molting in C. elegans is essential for larval growth and development and involves remodeling of the apical extracellular matrix of the epidermis (cuticle) through cycles of degradation and re-synthesis. Using a genetic approach, we identified two NIMA family serine/threonine kinases, NEKL-2 and NEKL-3, and three ankyrin-repeat proteins (MLT-2, MLT-3, and MLT-4), as essential for the completion of molting. Furthermore, genetic analyses indicate that nekl-2 and nekl-3 carry out partially redundant functions. NEKL-3 is highly conserved and very similar to mammalian Nek6 and Nek7, which regulate several cell cycle processes involving microtubules. Co-expression of mammalian Nek6 and Nek7 rescue molting defects in nekl-3 mutants, suggesting that these proteins share a conserved molecular function. Surprisingly, nekl-3 is not required for cell cycle regulation in C. elegans, but functions specifically in the epidermis to promote cuticle shedding, possibly through the regulation of cytoskeleton architecture, vesicular trafficking, or both. NEKL-2 is the most similar to mammalian Nek8, which may control microtubule organization during the formation of primary cilia. NEKL-2 functions specifically in the epidermis, a tissue lacking cilia, where it promotes the endocytosis of LRP-1/megalin, an essential molting factor and receptor for low-density lipoproteins. Furthermore, NEKL-2 functions as global regulator of clathrin-mediated endocytosis in the epidermis. Our data, together with studies of their mammalian orthologs, indicate that NEKL-2 and NEKL-3 associate with ankyrin-repeat proteins, which may function as scaffolds for NEKL-2 and NEKL-3 signaling. Loss of several conserved ankyrin-rich proteins (MLT-2/ANKS6, MLT-3/ANKS3 and MLT-4/INVS) leads to specific defects in molting similar to nekl-2 and nekl-3 mutants, and also show defects in LRP-1 trafficking. CRISRP-generated fluorescently labeled NEKL-2, MLT-2 and MLT-4 largely colocalize with each other in the main epidermal tissue of C. elegans. Correspondingly, NEKL-3 and MLT-3 show similar expression patterns and Y2H analysis indicates that NEKL-3 and MLT-3 physically interact. This interaction is important for the proper localization of NEKL-3 in the cytosol, as mlt-3 depletion leads to abnormal nuclear accumulation of NEKL-3. Interestingly, nekl-3, nekl-2 and mlt-4 defects are partially suppressed by cdc-42 depletion, suggesting that CDC-42 could be a target for negative regulation by the NEKL–MLT network, which may regulate trafficking and/or cytoskeletal organization during molting cycles. Taken together, our studies have identified several unique roles for NIMA family kinases that we expect are conserved in other eukaryotes, including mammals, but which have been largely overlooked.