Hybridization is a major force of evolution and has profound consequences due to increased heterozygosity and the creation of novel allele combinations. Hybrid zones form when allopatric taxa meet in secondary contact and hybridize. These allele combinations can be random, but sometimes alleles are retained nonrandomly leading to genomic architectures of hybridization. Genomic architectures of hybridization can be the product of natural selection, especially when present at significantly higher levels than expected by chance. Here we used three SNP data sets to identify hybrids in four genotypically distinct putative hybrid zones with unique environments. We identified genomic architectures of hybridization at the population, hybrid group, and all hybrids levels. We also found evidence for adaptation of hybrids to elevation and identified two hybrid populations that would be ideal for seeking direct evidence of local adaptation. We also developed SequelTools, which is a collection of tools for working with PacBio Sequel raw sequence data. This research in teosinte hybrids provides the hybridization and hybrid zone communities an excellent model study system and the creation of SequelTools makes using PacBio data much easier, which will help a large and diverse set of researchers take advantage of this powerful sequencing technology.