Non-coding RNAs (ncRNAs) are an increasingly large class of RNAs that play important roles in the cell, like control of protein synthesis, gene expression and regulation, pre-mRNA splicing, chromosome silencing, guide template for nucleic acid targeting, among others. The study of ncRNA families occurring in closely related species allows us to observe evolutionary transformations and mechanisms acting on functional regions of the genome beyond the constraints of protein coding regions. We studied five families of ncRNAs (snRNA, snoRNAs, SRP, RNaseP and telomerase RNAs) present in nine recently sequenced species of the Hemyascomycetes clade of yeasts. We observed patterns of strong sequence conservation in short functional regions (mainly guide sequences for target molecules) and sequence co-variation in structured regions, side-by-side with with highly divergent regions presenting great variation either in contest as length. Those observations confirm the ability of ncRNAs to keep structure and function in spite of significant sequence and structural variation allowing for an effective exploration of the sequence space.