The SEEDSTICK transcription factor is important for flower and seed development, but the underlying molecular mechanisms remain unclear in cotton. In this study, we identified and cloned two STK homolog genes in upland cotton, an economically valuable cultivated crop. Phylogenetic and sequence analyses showed that the C-terminus of both GhSTKs had a conserved -DJJILHLG amino acid sequence and that GhSTK1 and GhSTK2 were very similar to GaAGL11 and GrAGL11, respectively. Quantitative real-time PCR analysis revealed that both GhSTKs were highly expressed in the ovules, and GUS activity was detected in the style and stigma. Subcellular localization experiments showed that GhSTK1 and GhSTK2 were localized to the nucleus. In Arabidopsis, the overexpression of GhSTK1 or GhSTK2 affected floral organ development and seed formation by increasing the transcript levels of the CKX genes and other genes related to floral development. Silencing both GhSTK1 and GhSTK2 increased the expression of GhFT and GhSHP and led to the earlier appearance of cotton buds. Yeast two-hybrid and bimolecular fluorescence complementation assays indicated that the two GhSTK proteins could interact with the GhSEP3 and GhSEP4 proteins. The present results suggest that GhSTK1 and GhSTK2, which have different sequences and expression patterns, might be functionally redundant and influence the regulation of cotton bud and seed development.