Previous studies have described the molecular profiles and their relations between and within two major histologic subtypes, adeno and squamous cell carcinoma in many cancers. The differences in regulatory impact of miRNAs and epigenetic effect of methylation on gene expression were examined between the histologies using the cancer genome atlas (TCGA) studies on cervical cancer involving 31 cases of adeno and 144 cases of squamous cell carcinoma. First, the DE analyses for miRNA, methylation and their target mRNA between the histologies were carried out followed by multiple testing adjustments. Second, the correlation analyses between the selected miRNA and target mRNAs, and methylation and mRNAs were carried out within each histologic subtypes. A few miRNAs such as miR-205, miR-200 and miR-224 were found to have statistically significant anti-correlation with ERBB3, JAG1 and EYA4 respectively in squamous (p=0.0203, 0.0013, 0.0001) but not in adenocarcinoma. Also, methylation probes near these genes were significantly anti-correlated with corresponding genes in squamous histology only. This study attempts to provide new insights into the differences in gene silencing mechanisms.