Saccharomyces cerevisiae, the best-known representative of the Saccharomycotina subphylum, is an intron-poor organism with introns in only 5 % of its protein-coding genes. The most popular model of intron evolution suggests that intron-poor eukaryotes, such as S. cerevisiae, have undergone extensive intron loss throughout their evolutionary history. Against this background of intron loss, the retention of specific introns in the S. cerevisiae genome might be attributable to an evolutionary advantage that they provide. Introns have been shown to exhibit ‘function’ in various ways: through recognition of their sequence by RNA binding proteins, the adoption of secondary structures after transcription, the mechanism of splicing itself, and noncoding RNA genes embedded within them. In order to understand how RNA structures contribute to intron function, we first performed a computational screen using 306 alignments of S. cerevisiae intron orthologs. We identified conserved RNA structures in 19 introns that act either in trans as independent intron-encoded ncRNA genes or in cis within the pre-mRNA. Our results showed that introns with conserved secondary structures are conserved in yeast and experimental validation revealed they are frequently maintained in the cells after splicing. Our results suggest that the intron in GLC7 contains a novel ncRNA that regulates expression of its host transcript under stress conditions. Secondly, we focused on the HAC1 intron, which is known to be spliced upon the unfolded protein response by an endoribonuclease IRE1. We showed that the conservation of known intron-defining RNA hairpins in HAC1 extends to Fungi and Metazoa. Concurrently, we identified with high confidence those species that have lost the mechanism of this unconventional splicing. Thirdly, we investigated rates and mechanisms of intron loss within the whole Saccharomycetaceae family in order to develop our findings on the conservation of introns with RNA structures within the context of yeast evolution on both the species and clade level. Computational intron prediction supplemented by RNAseq data from four yeast species demonstrated that both intron loss and conservation of intronic ncRNAs were prevalent in yeast species, and that these patterns have been shaped by whole genome duplication. Lastly, we hypothesise that intron loss in recent yeast evolutionary history has been promoted by double strand break repair machinery.