Preparing the technology proficient learners to meet the needs of 21st century  has emerged as a critical challenge facing education in our country. The teacher has to prepare the young generation to fit in to the technology intensive society of the 21st century. Instructional design (ID) is the systematic process of planning events to facilitate learning. The ID process encompasses a set of interdependent phases including analysis of learners, contexts and goals; design of objectives, strategies and assessment tools; production of instructional materials; and evaluation of learner performance and overall instructional design effort (Gagne, Briggs, and Wager, 1992).The impact of learning solely depends on the efficiency of the teacher in delivering the message. But after the advent of multimedia technology the students have more wider opportunities through the multimedia namely computers, internet and A-V aids in equipping themselves with latest information and knowledge. A student in the higher learning is all set to be convinced by the teacher for transformation. In this vision, this paper makes its attempt to develop a multimedia based instructional design in Botany at undergraduate level and to determine the effectiveness of it with undergraduate students of science. The results reveal that the Multimedia based instructional design is effective and it can enhance the knowledge and understanding of the students as it is developed with combinations of text, audio, animation, images, video and pedagogical applications which are blended to visualize the content.