Aflatoxins are a class of mycotoxins that are of great agro-economic importance. Due to their health implications, and large economic burden, aflatoxins have become the most studied group of mycotoxins. A specific interest in rapid, robust, and cost effective, on-site sensing platforms for mycotoxin contaminants has been shown. Aptamers are functional oligonucleotide sequences that are selected to bind a cognate ligand with high affinity and selectivity. Novel structure switching aptamer candidates for total aflatoxin were previously selected. Electrophoretic mobility shift assays, melting temperature, and circular dichroism along with predictive structural characterization techniques were used to help elucidate the aptamer candidate's structural biases for G-quadruplex formation. Two candidates were determined to bind aflatoxin B1 (AFB1) with high affinity using microscale thermophoresis. Using the AFB1 binding aptamers, progress has been made towards developing FRET-based signalling sensors that leverage the structure-switching properties of the aptamer.