Phosphorylation is one of the critical protein modifications, which can lead to changing the activity of the proteins and regulating a variety of biological processes. Therefore, it is essential to properly maintain the phosphorylation level on proteins by balancing the activity of kinases and phosphatases. In this study, we report that calcineurin, a serine/threonine phosphatase, counteracts with a salt inducible kinase (SIK) to control male tail development in <i>Caenorhabditis elegans</i>. The counteracting regulation is cell lineage-dependent; the number of defective rays from T lineage in animals lacking calcineurin <i>
tax-6</i> is decreased by knock-down of SIK <i>
kin-29</i>. This result is in contrast with the knock-down of bone marrow protein (BMP) receptor kinase <i>
sma-6</i>, which slightly aggravates the T lineage defect. Also, <i>
sma-6</i> knock-down results in modest defect in ray 1 of V5 lineage in the absence of <i>
tax-6</i> activity. Finally, knock-down of a tyrosine phosphatase <i>
cdc-25.3</i> does not affect the defective ray phenotype of calcineurin <i>
tax-6 loss-of-function(lf)</i> mutants. Altogether, these results suggest that balanced phosphorylation mediated by <i>
tax-6</i> and <i>
kin-29</i> is required for proper development of T lineage rays, and <i>
tax-6</i> and <i>
sma-6</i> may function in a parallel pathway in the developmental process of V5 lineage ray 1. This study emphasizes the elaborated developmental process of male ray formation, in which carefully coordinated expression of various genes is essential.