Gerbera Hybrida is one of the important cut flowers across the world. The novel traits are the primarily market requirements and the breeding targets, mainly determined by the degree of genetic variation after hybridization. However, meiotic recombination is highly conserved in most eukaryotes which suppressed the crossover formation and limited the genetic diversity. Recently, several meiotic recombination suppressors have been identified and characterized in plants, whereas it remains elusive in G. hybrida. In order to characterize the expression patterns of these suppressors in G. hybrida, 20 candidate reference genes were identified from the transcriptome datasets of G. hybrida, and their expression stabilities during plant development were evaluated by geNorm, NormFinder and BestKeeper. Although the most stable reference genes were variable in different softwares, comprehensive ranking revealed that PGK2 was the most stable reference gene and GAPDH was the most un-stable one. The expression patterns of FANCM, FIGL1, RECQ4, RM1, and FLIP further validated that PGK2 was suitable for normalization of gene expression. Our study identified a reliable reference gene for gene expression during meiotic recombination, and provided functional insights into meiotic recombination suppressors in G. hybrida.