The genus Podophyllum (common name: May Apple) has high medicinal value due to the presence of anticancer molecule, podophyllotoxin. A total of 35 individuals belonging to three species of Podophyllum viz. P. hexandrum Royle, P. sikkimensis R. Chatterjee and Mukherjee both Indian species, and their American counterpart, P. peltatum L. have been investigated with a view to ascertain variation in their (1) podophyllotoxin content, and (2) molecular profiles generated through AFLP markers. The active principle content varied within the representative individuals of different populations of a species and between species; the species-wise podophyllotoxin content (% of dry wt) ranged as follows: P. hexandrum-Munsyari populations: 0.39–1.20 %, P. hexandrum-Kullu populations: 0.58–1.50 % (highest), P. peltatum: 0.50–1.30 %, and P. sikkimensis: 0.06–0.73 % (lowest). Detection of podophyllotoxin in P. sikkimensis, although at low levels, would appear to be the first report of its occurrence in this species. The genetic diversity and relationship amongst 35 sampled individuals of three species have been analyzed using 20 AFLP markers, which resulted into 1,358 loci of which 595 were polymorphic revealing 44 % polymorphism. High level of genetic diversity was observed (percent of polymorphic bands, PPB = 88.01 %; PIC = 0.813) among the species, while it was low within the individual species (PIC = 0.57 %; Marker index, MI = 4.77). Genetic similarity among the species (calculated with Euclidean coefficient) showed two major clusters. Cluster one contained all the individuals of P. peltatum (American May Apple) whereas cluster two grouped together individuals representing various populations, belonging to both the species of Indian May Apple (P. hexandrum, and P. sikkimensis). The observed paired relationship (45–50 % similarity; calculated from AFLP data) of intercontinental species in the Podophyllum group (P. hexandrum, and P. sikkimensis vs. P. peltatum) would appear to be paraphyletic. The AFLP data of the analyzed representatives have been used to examine the sister relationships among these species, and would be beneficial to find ways to strengthen the gene flow among populations to maintain the natural genetic variation within the populations of Podophyllum species.