The objective of the present work was to use MAS in self-pollinated cassava populations for obtaining individuals with high inbreeding (f) aimed at rapid development of partial inbred lines. Three progenies (F0222, F1378 and F1662) were self-pollinated, generating a total of 233 S1 individuals. The progenies and the S1 individuals were evaluated in the seedlings and clonal evaluation trials (CETs). In the CET, plants were evaluated for the following traits: plant height (PH), root dry matter content (DMC), above ground yield (AGY), root (RY) and starch yield (SY). Twenty-seven microsatellites and five minisatellites were used to determine the level of inbreeding of the S1 individuals. Inbreeding (f) values varied from 0.15 to 0.89 within progenies, whereas most of the S1 individuals presented f values above 0.50. In average, 25% of the S1 individuals were selected, which resulted in a 38% inbreeding increase in the cassava progenies. In contrast, phenotypic selection showed no differences in inbreeding increase. Furthermore, there was no correlation between the level of inbreeding and agronomic traits. MAS was efficient for the identification and selection of cassava S1 individuals, with higher inbreeding values contributing to the decrease in the breeding cycles necessary to obtain new cassava inbred lines.