The objective of this study is to find out the teacher’s perception on the implementation of using Whatsapp messanger and Youtube in class B 5th semesters of FLTM classroom at Muhammadiyah University students of Kendari. Since teacher’s perception has not been investigated thoroughly in the earlier research on the implementation of using WhatsApp and Youtube media as a learning tools.  This study employs qualitative study design to find out lecturer’s perception in teaching process using Whatsapp and Youtube.  The instruments used in this study are documentation and interview and the data are analyzed using data reduction, data display, meaning coding, meaning condensation, meaning interpretation, conclusion drawing and data triangulation.  The findings reveal that the teacher considered to implement Whatsapp and Youtube in teaching have several advantages and disadvantages in learning objective and outcomes. This can be viewed in the arrangement of knowledge of subject matter, teacher-students interaction, design of instruction, and course management. Furthermore, teacher’s beliefs in using Whatsapp and Youtube in teaching appeared to be strongly connected to the flexibility of teaching and learning process and learning content availability.