BackgroundThe clinical symptoms of invasive fungal infections (IFI) are nonspecific, and early clinical diagnosis is challenging, resulting in high mortality rates. This study reports the development of a novel aptamer-G-quadruplex/hemin self-assembling color system (AGSCS) based on (1 → 3)-β-D-glucans’ detection for rapid, specific and visual diagnosis of IFI.MethodsWe screened high affinity and specificity ssDNA aptamers binding to (1 → 3)-β-D-glucans, the main components of cell wall fromCandida albicansvia Systematic Evolution of Ligands by EXponential enrichment. Next, a comparison of diagnostic efficiency of AGSCS and the (1 → 3)-β-D-glucans assay (“G test”) with regard to predicting IFI in 198 clinical serum samples was done.ResultsWater-soluble (1 → 3)-β-D-glucans were successfully isolated fromC. albicansATCC 10,231 strain, and these low degree of polymerization glucans (< 1.7 kD) were targeted for aptamer screening with the complementary sequences of G-quadruplex. Six high affinity single stranded DNA aptamers (A1, A2, A3, A4, A5 and A6) were found. The linear detection range for (1 → 3)-β-D-glucans stretched from 1.6 pg/mL to 400 pg/mL on a microplate reader, and the detection limit was 3.125 pg/mL using naked eye observation. Using a microplate reader, the sensitivity and specificity of AGSCS for the diagnosis of IFI were 92.68% and 89.65%, respectively, which was higher than that of the G test.ConclusionThis newly developed visual diagnostic method for detecting IFI showed promising results and is expected to be developed as a point-of-care testing kit to enable quick and cost effective diagnosis of IFI in the future.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12941-023-00570-6.