This study examined the differences in cranial morphology of tree squirrel species (Heliosciurus rufobranchium) from four different locations in rainforest part of Nigeria. Locally fabricated live traps made of wire-mesh and steel were used to capture the squirrels. Trapped tree squirrels were immediately transferred to the laboratory in cages,where they were euthanized by placement in a bell-jar containing chloroform-soaked cotton wool. Individuals from two locations (33 from Ile Ife and 49 from Emure Ekiti) were then preliminarily identified to the generic level, usingan identification key. Eighty-two (82) skulls were prepared from them, using Long Island Natural History Museum Guide. The sexes of the specimens were determined by visual inspection of the external genitalia. Twenty-seven (27)cranial and six (6) external body parameters were measured using digital Vernier caliper. One-way analysis of variance at p<0.05 was used to determine the difference in measured body parameters and Principal Component Analysis was used to differentiate the measured skull parameters. The results showed that the body parameters; head body length,tail length, tail body length, ear length, hind foot length and body weight measured were slightly different from one location to another. Also, the cranial measurements showed some similarities and differences between the two locations (Ile Ife and Emure Ekiti). In conclusion, the cranial measurements of the tree squirrels from the two locations (Ile Ife and Emure Ekiti) showed slight differences despite the fact that the tree squirrels are from the same genus (H. rufobranchium).