Differences in physical and structural characteristics of seeds may indicate variability within and between plant populations. In the present study, we performed a close characterization of dimension, shape, and tegument delayed chlorophyll fluorescence in seeds obtained from three species of the genus Annona (Annonaceae), i.e., Annona coriacea, A. montana, A. squamosa. Results showed that studied seeds may be sorted as scalene ellipsoids expressing low values for the seed sphericity. The morphological estimates suggested differences in seed shape for all species. A high correlation was observed between surface area and volume (r2 > 99%) for all the three species suggesting that in addition to structural shape. In addition, we also observed very high positive correlations (Rho = 1.000, p < 0.001) between surface area and arithmetic mean diameterof the seeds for all species. The first principal component (PCA1) of elliptical Fourier descriptors explained most of the variations in morphological structure of the seeds in the three species. Additionally, a less intense tegument delayed chlorophyll fluorescence was observed for A. montana while the highest intensity was recorded for A. squamosa, revealing the potential use of fluorescence spectroscopy in discrimination at the species level by analyzing the frequency domain by means of Fourier Transform spectra as well as the relationship time-frequency of chlorophyll fluorescence. Keywords: Dynamics of fluorescence, Fourier descriptors, Structural traits, Phenomics