Maize is an important crop species that has been subjected to intensive breeding programs. Understanding the genetic diversity in maize is thus vital for crop improvement and breeding studies. We performed four different multi-allele detecting marker systems amplified fragment length polymorphism (AFLP), sequence-specific amplified polymorphism (SSAP), methylation-sensitive amplified polymorphism (MSAP), and transposon display methylation amplified polymorphism (TD-MSAP) to analyze genetic and epigenetic variation and diversity among dent, waxy, and sweet corn. The (epi) genetic diversity, (epi) genetic distance, gene flow, genetic frequency, cluster analysis, PCoA, and AMOVA analysis were calculated. Cultivar differentiation is well-established in maize, and the results suggest that not only genetic but also epigenetic variation is responsible for the differences obtained in maize cultivars. Estimates of genetic relationship were significantly correlated between the AFLP, SSAP, and MSAP datasets. The current study is the first report on the systematic comparison of TD-MSAP with the other marker systems. The genetic variation detected by TD-MSAP was higher than that calculated by AFLP, SSAP, and MSAP but was in discordance with accepted genetic relationships. These dissimilarities between TD-MSAP and other marker systems can be informative for understanding the genetic relationships between the species.