This paper presents an analysis of integrating morpho-syntactic theory in Indonesian interference which is influenced by lexical terms in L1 (Javanese) and L2 (Indonesian). The data were collected through questionnaires with a set of 12 open-ended questions, 14 durative texts containing interference in lecturer-student interaction, observation, interviews, and discussions with some experts in related research. This study involves 249 Indonesian undergraduate students who were majoring in English, and took speaking class, and joined presentations in content courses, together with their 10 English lecturers. The students and English lecturers conducted communicative classroom interactions in English teaching and learning process in IAIN and STKIP PGRI Tulungagung, East Java Indonesia. The data was analysed using a descriptive qualitative approach. The finding revealed that nine morpho-syntactic types and patterns of Indonesian interference are developed significantly with morpho-syntactic classification and properties including number, case, tense, mood, diathesis, agreement, comparative degree, aspect, and word class; three main patterns consisting of phrases (NP, VP, Adj P, Adv P), clauses and sentences. Interference is defined as the tendency to misuse English, which is students' L3 (third language) in student-student and student-lecturer interaction due to the influence of Indonesian and Javanese structures. The study also showed that both L1 and L2 could not be the predicting factors in interference occurrence. This may be attributed to their competence in acquiring a foreign language such as English. The results highlight that contextual English learning efforts based on students' needs and English lecturers' competence should be created. As English teachers and lecturers, they can make an effort by fulfilling the requirements as professional advanced models.