Introduction: This study was carried out to compare two retrograde filling materials entitled mineral trioxide aggregate (MTA) and Root MTA (RMTA) in regard to their marginal adaptation and surface defects. Method: In this study twenty extracted human teeth were used. In all teeth after cleaning and shaping, the root canals were obturated by gutta-percha and root canal sealer. After that in each tooth the 3 millimeter of root end was resected and a retrograde cavity was prepared. Then, the teeth were randomly divided into two experimental groups. In group I the retrograde cavities were filled by MTA and in group II the cavities were filled by RMTA. Then using Confocalmicroscope and stereomicroscope the location of the gaps between filling material and cavity walls was determined and measured by Autocad and Photoshop soft wares. Finally the obtained data were analyzed by One sided Fisher’s exact test. Results: There was a significant difference in marginal adaptation between two types of MTA (p<0.029). ٍOnly one tooth, in MTA group showed gap between cavity walls and root-end filling material, however, 60% of the teeth in RMTA group showed gap in their margins. In regard to surface defect there was a significant difference between the two groups (p=0.016). In MTA group 50% of the cases showed a defect on their surface, while in the RMTA group except one case, none of the cavities showed surface defect. Conclusion: It can be concluded that MTA has better marginal adaptation than RMTA.