Bidens pilosa L. var. radiata, an invasive plant in Taiwan, is distributed into mountain area. In contrast to B. pilosa var. radiata, B. pilosa var. minor is a naturalized plant and distributed mainly in mid-altitude of the island. This study aims to (1) investigate phenotypic variations between low- and mid-altitudinal populations of these two varieties of B. pilosa, and (2) evaluate the causes, environmental effect or genetic differentiation, of the variations. Two populations, one from low-(500 m) and the other from mid- altitude (1300 or1600 m) along an elevation gradient in central Taiwan, of both varieties were selected for the study. We compared ecophysiological traits of field populations and of progeny of these populations cultivated in a common garden. For both varieties, mid-altitudinal populations had significantly higher chlorophyll and N contents, more positive δ13C values and larger seeds than low-altitudinal populations. However, most of the phenotypic variations between altitudinal populations disappeared in common garden-grown plants. The results suggested that these variations were phenotypic plasticity in response to changes in environmental factors associated with altitudes. Comparing between populations of the same variety, seeds of the var. minor collected from mid-altitudinal population germinated faster. In contrast, seeds of the var. radiata from mid-altitudinal populations germinated slower and required more days to germinate. Thus, seeds produced by the mid-altitudinal population of the var. radiata had inferior germination performance, which might reduce its competitive ability at mid-altitude. However, high degree of phenotypic plasticity would allow B. pilosa var. radiata to spread into mountain area.