The demand for developing rapid and non-destructive techniques that is suitable to real-time and on-line detection of aflatoxin and fungal contamination has received significant attentions. Measurement techniques based on fluorescence spectroscopy (FS), near-infrared spectroscopy (NIRS) and hyperspectral imaging (HSI) have provided interesting and promising results for detecting aflatoxin and/or fungal contamination in a variety of foods. As such, the main goal of this article is to give an overview of the current research progress of FS, NIRS and HSI techniques in rapid detection of aflatoxin and fungal contamination in different varieties of agricultural products. These techniques are described in terms of their working principles, features and application advantages in detecting aflatoxins and fungal contamination. The research advances of each technique applied in different agricultural products are reviewed and the results obtained from different studies are compared and discussed. Perspectives on their future trends and challenges are also addressed.