G-Quadruplexes, a class of noncanonical but highly stable nucleic acid structures, have the potential to be part of the regulatory mechanism of cells. They can form in the genome where the double-stranded helix is unwound to facilitate formation of a G-quadruplex. The biological significance of these structures is yet to be understood entirely. This work presents a novel approach and investigates common characteristics in the distribution of G-quadruplexes relative to genes in plants through analysis of genomes and gene expressions. The results indicate that G-quadruplex distribution has gone through significant changes with the evolution of higher plants and, for the first time, that G-quadruplexes enriched at the beginning of introns may have a regulatory role during transcription.