The chief aim of plant breeding is to improve varieties so as to increase their yield and breeding traits. One of the first stages of breeding is the selection of parental forms from the available gene pool of existing varieties. To date, costly and laborious methods based on multiple crossbreeding and phenotypic selection have been necessary to properly assess genetic resources in terms of productivity, quality parameters, and susceptibility to biotic and abiotic stressors. The often long and complicated breeding cycle can be significantly shortened through selection using DNA markers. To this end, use is made of close couplings between the marker and the locus responsible for the inheritance of the functional trait. The aim of this study was to identify single nucleotide polymorphism (SNP) and SilicoDArT markers associated with yield traits and to predict the heterosis effect for yield traits in maize (Zea mays L.). The plant material used in the research consisted of 19 inbred maize lines derived from different starting materials, and 13 hybrids resulting from crossing them. A two-year field experiment with inbred lines and hybrids was established at two Polish breeding stations on 10 m2 plots in a randomized block design with three replicates. The biometric measurements included cob length, cob diameter, core length, core diameter, number of rows of grain, number of grains in a row, mass of grain from the cob, weight of one thousand grains, and yield. The isolated DNA was subjected to DArTseq genotyping. Association mapping was performed in this study using a method based on the mixed linear model with the population structure estimated by eigenanalysis (principal component analysis of all markers) and modeled by random effects. Narew, Popis, Kozak, M Glejt, and Grom were the hybrids used in the study that showed the highest significant heterosis effect in 2013 and 2014. The similarity between parental components determined on the basis of SNP and SilicoDArT marker analysis did not exceed 33%. It was found that the genetic similarity between parental components, determined on the basis of SNP and SilicoDArT markers, reflected their degree of relationship, and correlated significantly with the effect of heterosis. As the results indicate, the parental components for heterosis crosses can be selected based on genetic similarity between parental components evaluated using SNP and SilicoDArT markers, supported with information on the origin of parental forms. Of the markers we analyzed, 76 were selected as being significantly associated with at least six traits observed in 2013 and 2014 at both the Łagiewniki and Smolice stations.