Acid phosphatase genes are present in most Ascomycete genomes and are related based on sequence similarity to the PHO5 gene in Saccharomyces cerevisiae. In S. cerevisiae, PHO5 is regulated by inorganic phosphate starvation, and PHO3 (a PHO5 homolog) is regulated by thiamine starvation. Candida glabrata does not have PHO5 homologs. Previously, we determined that PHO5 was functionally replaced in C. glabrata with the PMU2 gene, which is part of a three gene family tandemly duplicated on chromosome 11. Using RNA-seq, we now determine that PMU3 is highly induced during thiamine starvation, that induction is dependent on the thiamine starvation regulators, THI3 and PDC2, and that PMU3 encodes a thiamine pyrophosphatase (TPPase). We determined that only Pmu3p (and not Pmu2p or Pmu1p) is a TPPase using a functional assay with thiamine pyrophosphate (TPP) as a sole source of thiamine that can only be accessed by TPPase activity. The RNA-seq data demonstrate that ten genes are highly induced during thiamine starvation and are THI3 dependent in C. glabrata. Unlike S. cerevisiae, the regulator THI3 is not induced during starvation, and additionally, C. glabrata does not have a THI2 homolog. We have characterized the highly inducible thiamine-regulated promoters using promoter-YFP fusions and flow cytometry and identified a minimal region that confers thiamine regulation. We expect that this promoter region binds CgPdc2 during thiamine starvation. The induction of both phosphate- and thiamine-regulated genes require chromatin remodeling/modification complexes for full induction of gene expression because mutants in Cgsnf2Δ, Cggcn5Δ, and Cgasf1Δ are aberrant in the regulation of phosphate- and thiamine-regulated promoters. We observe that C. glabrata has de novo sub-functionalized phosphatase expression into two tandem genes and because this system has analogous behaviors and characteristics to PHO5 & PHO3 in S. cerevisiae, there might be selective reasons for this sub-functionalized phosphatase architecture.