The lateral suppressor (Ls) genes have a conserved role in axillary meristem initiation in diverse plants. Transgenic chrysanthemum (Dendranthema × grandiflorum) carrying antisense Ls cDNA was generated using Agrobacterium-mediated transformation. Totally 139 shoots were obtained as transformants, and with 5 transgenic plants selected in the preliminary observation, shoot branching was screened on 3 different planting dates. The number of axillary buds in the transgenic plants was changed over season. Axillary buds were visible in all axils in the April planting, but the number of axillary buds was reduced in the June planting in 3 transformants. The biggest reduction in the number of axillary buds was found in Ls80, whose antisense Ls transcript was the highest. The percentage of axillary buds in Ls80 decreased from 100% to 26% when the planting date was delayed from April 26 to June 15, but increased again to 55.9% on the August 12 planting. Anatomical assay suggest that the loss of axillary buds was as a result of defects in initiating axillary meristem. Transgenic plants carrying the Ls antisense gene displayed several floral morphological differences in comparison with nontransgenic control ‘Jinba’. Typical abnormal features in the plants included lobbed petals and a stamen-like structure around the style. We conclude that the Ls gene has a conserved role in axillary meristem initiation in chrysanthemum and might interact with other temperature-dependent genes.