Apomixis is an asexual mode of reproduction through seeds. The morphological events that lead to apomictic reproduction occur within the ovary. Identifying genes that are differentially expressed in ovaries of sexual and apomictic plants is a strategy to understand apomixis at the molecular level. We have previously characterized apomictic and sexual accessions of Brachiaria brizantha, a forage grass of economical importance for cattle production in Brazil, to use as a system for comparative gene expression studies. This work shows the characterization of two sequences of a RNA-seq library that showed differential expression. Analysis using quantitative PCR showed that contig 2251 has a higher expression (2.3x) in ovaries of the sexual plant relative to apomictic plants, while contig 3298 has three-fold higher expression in ovaries of apomictic plants relative to sexual. Both contigs showed higher expression in anthers and roots compared to leaves. Contig 2251 shows, in available databases, similarity to ribosomal protein S27a-1 from Oryza sativa. In Nicotiana benthamiana this protein plays a critical role in the allocation of meristems cells that differentiate into lateral structures such as leaves and flowers. Contig 3298 shows similarity to ribosomal protein 5S. A semi-dominant mutation in Arabidopsis RPS5 gene causes growth retardation, floral and vascular defects and embryo lethality. The localization of the transcripts inside the ovaries of sexual and apomictic B. brizantha by in situ hybridization will be shown. The identification and analysis of genes with strong expression in ovaries may contribute to the understanding of embryo sac development and plant reproduction.