With characteristics of few seeds and high content of effective components in the fruit, dwarf habit, and strong stress resistance, polyploid plants plays an important role in crop and fruit tree breeding. Sweet orange ‘Licheng’ is a high-quality variety bred independently in China, which produces fruits with mostly monoembryonic seeds and a few polyembryonic seeds. So far, there are no reports about the polyploidy of this variety and the heterozygosity of its monoembryonic seeds. In this study, the screening, and genetic identification and analysis of polyploidy were carried out using sweet orange ‘Licheng’ as material. Two triploid and one tetraploid plants were selected by flow cytometry and chromosome microscopy from seedlings grown from naturally produced monoembryo seeds. Through the analysis of polyploidy by InDel markers, it was confirmed that these polyploids were grown from sexual embryos, and the proportion of homozygous loci was high, which may be caused by second meiotic division restitution (SDR) and post-meiotic genome doubling (PMD). Polyembryonic/monoembryonic molecular marker (MITE-P2) analysis showed that the clear short fragments and fuzzy long bands obtained from the genomic DNA amplification of ‘Licheng’ may be related to its ability to produce polyembryonic seeds, while the clear short bands only, obtained from the genomic DNA amplification of the three polyploid progenies, may be due to their inability to produce polyembryonic seeds. This study indicated that the proportion of polyploids in the progeny of ‘Licheng’ was high, with sexual polyploids obtainable from the monoembryonic seeds of ‘Licheng’, and monoembryo tetraploids obtainable from the progeny of ‘Licheng’, which provides an important reference for breeding of polyploids and monoemnryonic tetraploids with ‘Licheng’ as the parent.