Metadiscourse markers are aspects of a text which exclusively guide readers toward the meanings intended by the author. The present study aimed to investigate the organization of metadiscourse markers across scientific genre in Persian and English. It also attempted to explore the frequency of the two types of metadiscourse markers in English and Persian. The data for this study were supplied through different text types of scientific genre, such as biology, geology, chemistry, physics and mathematics. Out of the existing scientific textbooks in English and Persian, 20 books were randomly selected. The materials were originally written in English or Persian. In order to have ample instances of texts, 2 paragraphs of about 150 words were selected from each book. By analyzing the collected data, it was found that there is a relation between English and Persian in using metadiscourse markers. Both languages used high degree of metadiscourse markers, which contributed to their homogeneity in terms of metadiscourse usage. The findings also revealed that the average frequencies of the two types of metadiscourse are relatively different in Persian and English languages.