The opportunistic pathogen Candida glabrata shows a concerning increase in drug resistance. Here we present the analysis of two serial bloodstream isolates, taken 12 days apart. Both isolates show pan-azole resistance and echinocandin resistance was acquired during the sampling interval. Genome sequencing identified 9 nonsynonymous SNVs between the strains, including a S663P substitution in FKS2 and previously undescribed SNVs in MDE1 and FPR1, offering insight into how C. glabrata acquires drug resistance and adapts to a human host.