The research investigates the link and networks of Iranian research institute websites using webometrics and the link analysis method. The population includes the websites of 23 research institutes and centers in Iran. The data were collected using the Webometric Analyst software. The network diagram shows the mutual link strength among the set of research institute websites in Iran, and depicts the pattern of internal relationships among these websites. Iranian research institute websites are not in good conditions in link exchange and the cooperation with each other. In addition, the colink diagrams illustrated the covert relationships among Iranian research institutes suggesting that the common topics and contents have been the most important elements of colink creation among Iranian research institute websites. It was found that the websites of Scientific Information Database (SID), Iranian Research Institute for Information Science and Technology (IRANDOC), and National Library and Archives of I.R of Iran (NLAI) were in a better condition than those of other websites as regards the total in-links and out-links. Also, the first to the third ranks were dedicated to IRANDOC, SID, and NLAI websites respectively in in-link numbers and visibility. The analysis of Uniform Resource Locators (URLs) of in-links and out-links of Iranian research institute websites showed that the maximum number of in-link to these websites was reserved for the domains .ir and .com. The websites of Iranian research institutes and centers dedicated most of their out-links to scientific, religious, and fun websites, followed by the ones for universities and the institutes of higher education.