Aim: The purpose of this study was to evaluate the sealing ability of Biodentine and Endo Sequence with 17% EDTA and carboxymethyl chitosan (CMC) as retrograde smear layer removing agents using scanning electron microscopy (SEM). Materials and Methods: Forty human single rooted teeth were taken. Crowns were decoronated and canals were obturated. Apically roots were resected and retrograde cavities were done. Based on the type of retrograde material placed and the type of smear layer removal agent used for retrograde cavities, they were divided into four groups (N = 10): Group I 17% EDTA with Biodentine, group II CMC with Biodentine, group III 17% EDTA with Endo Sequence, and Group IV CMC with Endosequence. All the samples were longitudinally sectioned, and the SEM analysis was done for marginal adaptation. Statistical Analysis: Kruskal-Wallis and Mann-Witney analysis tests. Results: SEM images showed the presence of less gaps in group IV, i.e., CMC with Endo Sequence when compared to other groups with statistically significant difference. Conclusion: Within the limited scope of this study, it was concluded that Endo Sequence as retrograde material showed better marginal sealing ability.