In general, facial image-based remote photoplethysmography (rPPG) methods use color-based and patch-based region-of-interest (ROI) selection methods to estimate the blood volume pulse (BVP) and beats per minute (BPM). Anatomically, the thickness of the skin is not uniform in all areas of the face, so the same diffuse reflection information cannot be obtained in each area. In recent years, various studies have presented experimental results for their ROIs but did not provide a valid rationale for the proposed regions. In this paper, to see the effect of skin thickness on the accuracy of the rPPG algorithm, we conducted an experiment on 39 anatomically divided facial regions. Experiments were performed with seven algorithms (CHROM, GREEN, ICA, PBV, POS, SSR, and LGI) using the UBFC-rPPG and LGI-PPGI datasets considering 29 selected regions and two adjusted regions out of 39 anatomically classified regions. We proposed a BVP similarity evaluation metric to find a region with high accuracy. We conducted additional experiments on the TOP-5 regions and BOT-5 regions and presented the validity of the proposed ROIs. The TOP-5 regions showed relatively high accuracy compared to the previous algorithm’s ROI, suggesting that the anatomical characteristics of the ROI should be considered when developing a facial image-based rPPG algorithm.