Abstract: To observe similarities and differences in stem anatomical structures among litchi, longan and longli, we compared the stem transverse structures and vessel elements of 20 different materials among litchi, longan and longli by free hand section and tissue segregation procedure, respectively. The results showed that (1) The stem structure of the experimental materials from the inside to the outside was periderm, cortex, vascular tissue, pith and ray, but their structure characteristics exhibited great differences. Average pith rate of longan germplasm (26.19%) was significantly greater than that of longli (22.43%) or litchi (6.96%) germplasm, and among them the lowest pith rate was found in Litchi chinensis var. fulvosus (3.37%), followed by ‘Sanyuehong’ (14.14%), and wild longan (30.27%). In addition, the bark rate of litchi (41.93%) was significantly greater than that in longan (33.21%) and longli (29.83%). (2) Vessel density of each tested material was not obviously regular, with ‘Sanyuehong’ (93.17 No./mm²) exhibiting minimum vessel density, followed by longli (101.78 No./mm²); total vessel area/xylem area of litchi was significantly higher than that of longan and longli; the ‘Sanyuehong’ (22.13 μm) ray was significantly wider than that of the other tested materials. (3) Vessel elements mostly belonged to pitted or reticulate vessels, but did include a few ringed, spiral or scalariform vessels in the 20 accessions. Vessel diameter of ‘Sanyuehong’ (35.97 μm) was significantly higher than that of the other tested materials, followed by longli (33.90 μm), with and L. chinensis var. fulvosus (238.52 μm) significantly longer than other specimens. (4) The vessel elements of large aperture, short, end wall of small inclination (or level), no tail, pitted pattern, and simple perforation plate were evolutionary vessel element traits. In litchi germplasm, the vessel elements of ‘Sanyuehong’ were evolutionary, and L. chinensis var. fulvosus was more primitive. (5) Cluster analysis of the stem index structures found that the 20 accessions were firstly divided into two categories. The first category was Litchi germplasm resources, except ‘Sanyuehong’, and the second category included all longan germplasm resources, longli and litchi ‘Sanyuehong’. These two categories were then divided into eight groups, with each group having significant features alone. Comparison of species anatomical stem features showed that litchi was more primitive than longan, and longli was in the middle.