In this paper we discuss, with a new analysis of published data, the phylogenetic hypothesis of two genotypes of Taenia solium previously suggested. Sequences of mitochondrial (co1, cob, nad) and nuclear (18S+ITS1+5.8S, LMWA1 and LMWA2) T. solium DNA from Africa, Asia, Latin America, and Oceania deposited in GenBank international databases were analyzed for diversity and genetic structure. Overall, we found that percentages of polymorphic and informative sites were comparatively less in mitochondrial genes, and minimum or null values of nucleotide diversity and nucleotide polymorphism were also observed. Analysis of co1 populations showed two associations of particular interest: Asia/Latin America and Africa/Latin America; with minimal differentiation between them and a constant genetic flow. Bayesian phylogenetic trees built with the available sequences for co1+cob showed two clusters, one for Asia and another one for Africa/Latin America while with ribosomal sequences only one cluster was obtained that grouped Asian and Latin American populations. The haplotype network tree built using co1+cob showed two major clades, one clustering African and Latin American parasite populations and the other grouping Asian populations, hallmarking Mexican/Peruvian and the Indian populations as dispersion centers, respectively. The haplotype network tree built with ribosomal sequences exhibited Philippines and Peru/Mexico/Colombia as the two major dispersion centers, with several Latin American haplotypes diverging from the latter. Our results suggest that the gene flow within the different T. solium populations has the same dispersion pattern than the main maritime trade routes used between the XV and XIX centuries.