Archaeobotanical investigations at three riverine shell midden sites dating to the early Holocene – Baozitou, Shichuantou and Nabeizui – in the Yongjiang River Basin, Guangxi, southern China have identified charred fragments of archaeological parenchyma. A subset of the archaeological parenchyma was assessed using X-ray micro-computed tomography (microCT), which enabled virtual histological examination of the interior of parenchyma fragments. The microCT scanning identified a fragment of lotus root (Nelumbo nucifera), a possible immature fig fruit (poss. Ficus sp.), cooked food fragments, and less diagnostic elements, some of which derive from underground storage organs (USOs), including a bud/bulb and potentially an aroid. The fragment of lotus root from Nabeizui was directly radiocarbon dated using Accelerator Mass Spectrometry to 8770–8544 cal BP. A new AMS radiocarbon chronology based on Canarium nutshells for the three sites indicates that they were all used during the early Holocene. These findings contribute to the understanding of broad spectrum plant use by hunter-gatherer-fisher communities in southern China during the early Holocene, as well as showing the potential of microCT imaging for the analysis of archaeological parenchyma from this region.