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The analysis of seeds from archaeobotanical assemblages is essential for understanding the history of crop cultivation. However, the majority of these seeds are typically found charred, a condition that not only degrades DNA, which hinders genetic studies, but also distorts their morphological features, which may bias comparisons with uncharred modern samples. While the effects of charring on several other crop seeds or fruits are well-documented, date palm seeds remain largely unexamined, limiting our ability to use charred seeds effectively to document the agrobiodiversity dynamic of this crop. In this study, we assessed the morphological changes induced by the charring of 1375 Phoenix seeds under varied conditions, including charring temperatures of 200–600 °C, exposure durations from 10 to 120 min, and oxidizing/reducing conditions. By comparing charred samples with a modern reference collection of 6991 seeds, we evaluated the extent to which charring affects the ability to discriminate between groups of interest, particularly between wild and domesticated specimens. Our study identified a significant shrinkage in Phoenix seeds, up to 25%, as a result of charring, with the extent of deformation influenced by the conditions of exposure. The shrinkage displayed an isometric pattern, keeping the proportions between seed dimensions consistent, thereby validating size ratios as a dependable metric for studying Phoenix agrobiodiversity even when dealing with charred material. Moreover, seed outlines stay predominantly unchanged, further endorsing their utility in morphometric studies. Using our results to examine 13 charred seeds from Shahi Tump and Miri Qalat, two Protohistoric settlements (5th-3rd millennia BCE) located in the Kech-Makran district of southwestern Pakistan, we deduced a predominance of wild resource utilization over the cultivation of date palms. This research sheds light on the impact of charring on seed morphology and underscores its potential in differentiating between species and groups. It moreover confirms the value of charred seeds as a crucial resource for unraveling the complex history of crop cultivation, offering a detailed framework for future studies in this domain. • Date palm seed size is drastically impacted by charring but the deformation is isometric. • Date palm seed shape (outline) is not impacted by charring. • The date palm was not locally cultivated in the Makran region in the 3rd mill. BCE. [ABSTRACT FROM AUTHOR]