Azolla, a floating aquatic fern, turns red under some conditions. Two Azolla species, one native and the other introduced, with distinct morphology are found in Taiwan. The taxonomy of the introduced species is still suspicious. In addition, populations of the introduced species seem to expand. In this study, the DNA sequence data from four plastid loci (rbcL, atpB, rps4, and rps4-trnS) of populations of the two Azolla species were first analyzed to clarify the phylogenetic relationships. We then compared growth and physiological traits of the two species grown outdoors under two light treatments. The result of cladistic analyses showed that populations of the native species are at the same group with A. pinnata in China and Malaysia; in contrast, populations of the introduced species have the closest relationship with A. mexicana in south America. Accordingly, the native and introduced species are identified as A. pinnata and A. mexicana, respectively. A preliminary experiment conducted in winter of 2015 revealed that A. mexicana had higher relative growth rate (RGR), specific leaf area (SLA) and nitrogen content (%) than A. pinnata, but both species had similar chlorophyll content and photosynthetic traits. Accordingly, the difference in RGR of both species under sun treatment might due to their difference in SLA.