Turkey is an important citrus-producing country. However, new cultivars are needed to sustain citrus production and ensure its competitiveness against other crops. There are currently several citrus breeding programs that aim to help overcome the lack of local commercial varieties and to contribute CO Turkey's competitive capacity in the citrus market. In this study, we report the utilization of molecular markers in one such breeding program. Simple sequence repeat (SSR) markers were employed to eliminate nucellar individuals from a hybrid population produced by crossing. The crosses included 'Fremont' and 'Robinson' mandarins as the female parents and 'Midknight Valencia', 'Rhode Red Valencia', and 'Valencia Late' oranges and 'Rio Red' grapefruit cultivars as the male parents. Seedlings with the same banding patterns as the female parent were identified as nucellar seedlings by 11 SSR primers. Primers AG 14 and TAA03 were found to be more effective at identifying zygotic individuals than other primers. 'Fremont' and 'Robinson' mandarins produced 36.91% and 31.09% of nucellar seedlings, respectively. As a pollen parent, 'Rio Red' grapefruit had a higher ratio of zygotic seedlings compared to 'Midknight Valencia', and can be recommended in breeding programs. Comparative analysis of different citrus fruits in the breeding programs allowed us to design an efficient hybridization scheme for this study.