Background Protein kinase C iota (PKC iota) and protein kinase C zeta (PKC zeta) are two atypical protein kinase (aPKC) enzymes that contribute to cell proliferation and cancer development. The Hippo/YAP pathway is commonly disrupted and upregulated in cancers. Herein, the expression patterns and clinical relevance of PKC iota and PKC zeta are evaluated in relation to YAP, a downstream effector of Hippo, in lung adenocarcinoma (LAC). The protein and mRNA expression levels of PKC iota, PKC zeta, YAP, and their phosphorylated forms, namely p-PKC iota, p-PKC zeta and p-YAP, are evaluated in relation to clinicopathological factors, including patient survival. Methods A total of 200 primary LAC tissue samples were examined by immunohistochemistry for PKC iota, p-PKC iota, PKC zeta, p-PKC zeta, YAP, and p-YAP protein expression. Sixty pairs of LAC and non-neoplastic lung tissue samples were assessed for PRKCI, PRKCZ, and YAP mRNA levels. PKC iota, p-PKC iota, PKC zeta, and p-PKC zeta protein expression were evaluated by Western blot analysis in the PC9 and PC9/GR LAC cell lines with YAP modulation. Results LAC demonstrated cytoplasmic PKC iota, p-PKC iota, PKC zeta, and p-PKC zeta immunostaining patterns. Positive aPKC protein expressions were related with poor patient survival. Especially, increased p-PKC iota protein expression was significantly correlated with higher pathological stage and shortened overall survival. YAP overexpression contributes phosphorylation of PKC iota and PKC zeta protein expression in the LAC cell line. Conclusions PKC iota and PKC zeta are related to YAP in LAC. PKC iota and PKC zeta play distinct roles in LAC; specifically, p-PKC iota overexpression is suggested to underlie factors that indicate a poor prognosis.