In recent years, plantation areas are criticized for the reduction of species diversity and deterioration of habitat quality. The effects of stone pine (Pinus pinea L.) plantations on species diversity were investigated in this study to enlighten the situation. A total of 73 sample areas were investigated from north western Turkey (Biga-Canakkale) region, including 25 native and 48 plantation areas. Taxa of the sample areas were identified and species diversity and similarity analysis was performed. We found significantly lower number of plant species at plantation areas than natural areas at Pekmezli (4 yr old stand) and Kargi Ciftligi (25 yr old stand) blocks with p values 0.016 and 0.005 respectively. Shannon-Wiener index values of plantation areas were found to be 3.04 and 3.23 with p values 0.027 and 0.007 in Pekmezli and Kargi Ciftligi respectively. The Sorensen similarity analysis showed that, there was a higher similarity pattern in natural areas than in plantation areas. It was concluded that the plantation activities only in the areas of Pekmezli and Kargi Ciftligi negatively affected the number of species and diversity index values.