Misconception sabotages the meaningful learning. Young learners can have misconceptions about the science concepts with which they interpret their new experiences, hampering the development of canonical scientific knowledge. Identifying and remediating the misconceptions of the learners is an important task as an educator. Therefore, this study aimed to explore the misconceptions of the 9th grade students on particulate nature of matter (PNM) concept and effectiveness of the use of video animations in remediating those misconceptions. The study adopted a mixed method approach. The sample consisted of 20 students studying in 9th grade of Daga Central School in Bhutan. The misconception was identified using the certainty of response index (CRI) diagnostic technique. The study revealed 10 kinds of misconceptions held by students related to PNM, under the four themes, i.e., All matter is made of discrete particles, Space between the particles is empty, Particles are in constant random motion, and Bonds or forces exist between particles, the number of students' having misconception on the particulate nature of matter concept reduced considerably in the post-test after the use of video animations as the intervention. The study also revealed that most of the misconceptions that student possesses were rooted in their inability to understand the chemical concepts from macroscopic, sub microscopic, and symbolic perspective. The study contributed in two aspects: first, the study identified four themes in which students had misconceptions, alerting educators to be cognizant when involving in discourse of PNM concepts. Second, the study suggests that use of video animations as a potent strategy to teach PNM concepts to help students develop the canonical scientific knowledge on PNM concepts, as demonstrated by this study.