Recently (~ 100 years) formed allopolyploids Tragopogon mirus and T. miscellus and their diploid parental species, T. dubius, T. porrifolius, and T. pratensis, offer a rare opportunity to study the earliest stages of allopolyploidy. This study is the first large-scale common-garden experiment to assess trait variation in the entire North American Tragopogon allopolyploid complex. The allopolyploid species were resynthesized in 2009, allowing direct comparisons between the youngest possible allopolyploid lineages and their natural, established counterparts in natural populations of the Palouse Prairie in Washington and Idaho. For the first time we compare phenotypic traits on a large scale in Tragopogon in the same greenhouse study over an 18-month period. Our large common-garden experiment measured traits in growth, development, physiology, and reproductive fitness and analyzed differences between allopolyploids and their parental species and between synthetic and natural allopolyploids. As previously observed in many polyploids, the allopolyploid species had some larger physical traits and a higher capacity for photosynthesis than diploid species. Reproductive fitness traits were variable and inconsistent between the two allotetraploids, but results were clouded by insect infestations in the floral structures, ultimately reducing our sample size. Allopolyploids had intermediate phenotypes compared to their diploid parents in flowering time, petal color, and number of mature seeds per inflorescence. The three generations of resynthesized and natural allopolyploid lines generally showed minor to non-existent trait differences, therefore allowing us to conclude that any trait differences due to polyploidization were seen in the very first generation after allopolyploidy had occurred and did not change much in subsequent generations after polyploidy. It is important to note that T. dubius, one of the three possible parents in the complex, often over-produced in the traits measured, which disrupted the significance or trends of some phenotypes observed in this study. Something that might have been less of a problem if the experiment had been done on-site in a common garden experiment in the Palouse Prairie itself. In conclusion, in Tragopogon, allopolyploidy results in some predicted and expected phenotypic changes, such as gigas effects seen via increased total biomass, seed weight, number of flowers per plant, and photosynthetic capacity. Being polyploid did not produce a significant reproductive advantage, except for increased number of mature seeds per inflorescence, but did show an advantage in early seedling growth and primary vegetative growth in the first-year basal rosette. Polyploid germination was more variable than diploid, which was predicted by known meiotic aberrations already observed in this complex. We can conclude from this study that polyploidization contributes to progeny (larger seeds = larger seedlings) and establishment of the young plant, as well as the already known gigas effect observed in mature polyploid plants, resulting in increased competitive ability.