The information characteristics of AFLP and ISSR techniques were compared in the analysis of length polymorphism of gamma-treated mutant lines of Amaranthus cruentus and Amaranthus hypochondriacus x Amaranthus hybridus. Both of the techniques are widely used in the manner of universal marker system suitable for the analysis of any plant species, but differ in the time needed for the analyse and costs. Binary data matrices were used for statistical analyses. Cluster analysis was performed in UPGMA method using Euclidean distance to construct dendrograms and principal component analyses was used for generated data, too. Comparison of techniques was made on the graphs obtained from result of PCA and dendrograms that were obtained from results of cluster analysis. Matrix comparisons of Mantel test, for the correspondence of the similarity matrices was performed for the null hypothesis that there is no association between similarity matrices. In the analyzed set used in this study, ISSR primers produced 59% polymorphic bands, while AFLP primers produced 48% polymorphic bands and both of techniques were similar in their obtained information characteristics.