Most lizards in the Superfamily Iguanoidea have an XX/XY sex determination system in which sex chromosomal linkage has homology with chicken (Gallus gallus) chromosome 15 (GGA15); however, sex chromosome genomics remains largely unexplored due to the presence of homomorphic sex chromosomes in many species. Recent advances in high-throughput sequencing with genome complexity reduction now provide an effective approach to identify sex-specific loci in both single nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA), and a better understanding of sex chromosome dynamics in this lineage. Here, we applied Diversity Arrays Technology (DArTseq™) in 29 phenotypic sex assignments of green iguana (Iguana iguana). We confirmed a male heterogametic (XX/XY) sex determination mode in this species, identifying 29 perfectly sex-linked SNP/PA loci and 164 moderately sex-linked SNP/PA loci, likely serving as evidence indicative of XY recombination. 3 loci from perfectly sex-linked SNP/PA loci showed partial homology with several amniote sex chromosomal linkages. Our results support the hypothesis of an ancestral super-sex chromosome with overlaps of partial sex chromosomal linkages. However, only one locus from moderately sex-linked loci had homology with GGA15, suggesting that the specific region homologous to GGA15 was located outside the non-recombination region but very close to this region of sex chromosome in the green iguana. The location of GGA15 might, therefore, be further apart from the putative sex-determining locus in green iguana. The DArTseq platform provides an easy to use strategy for future research on sex chromosome evolution of lizards in Iguanoidea, particularly for non-model species with homomorphic or very cryptic sex chromosomes.