Floral development, directly related to the progeny reproduction and species continuation of plants, is an important stage in the lifespan of angiosperms. The MADS-box genes play a key role during the floral development. In this study, a new member of MADS-box family gene HaAGL11 was identified from the sunflower transcriptome datasets. Phylogenetic analysis showed that HaAGL11 gene was closely homologous with the AGL16 gene in Arabidopsis thaliana. Moreover, the expression pattern at different stages of flower development revealed that HaAGL11 gene was highly expressed at the late maturation stage of floret organs, flowering stage, and early embryonic development stage. The expression analysis in floret tissues indicated that HaAGL11 was highly expressing in the ovary of late maturation stage and flowering stage. Thus, this result suggested that HaAGL11 gene might be associated in regulating the development of ovary and fruit in the late stage of flower development and it could lay a foundation for preliminary exploration on the regulatory role of HaAGL11 gene in flower development and fruit formation of sunflower, beneficial for further investigating the molecular regulation mechanism of growth and development of sunflower, and providing some guidance data for the genetics and breeding of sunflower.