There is considerable confusion concerning the structure and synonymity of macroscopic sarcocysts in goats. In the present work, ultrastructural and molecular study on fat and thin macrocysts of Sarcocystis isolated from naturally infected goats were investigated. Two forms of macrocystic sarcocysts were collected from fresh oesophagus, diaphragm, skeletal muscles and heart of slaughtered goats in abattoirs of Tehran and Ghazvin provinces of Iran. Then ultrastructural and molecular studies were carried out contemporaneous using PCR technique and transmission electron microscope respectively. Based on morphological examinations both cysts differ in shape with naked eye but they had the same wall structure with electron microscopy study. The 18S rRNA amplification by PCR showed a 637-bp band for both forms. The results of sequencing of PCR product of the cysts indicated these two kinds of cysts were identical to each other and also to Sarcocystis moulei. The present result, suggests that fat and thin cysts are the same and identical species.