This article analyzes the correlation between the use of functions of citations and the organizational structure of the Introduction section of a corpus of sixteen (16) master´s theses written in Spanish in the field of Applied Linguistics by native and non-native writers. The quantitative and qualitative analysis in this study arises from the model proposed by Carbonell- Olivares et al. (2009) which aims to define the organization of the Introduction section of the doctoral thesis in Spanish and the classification of the functions of citations made by Sánchez Jiménez (2011). The research results show that there is a direct relationship between the use of citations and rhetorical organization of the master´s thesis. On the other hand, it is indicated that the formal instruction received by Filipino students makes a significant difference both in the order of the Introduction section and in the quantity and variety (AT, AP, REF, DE, EN, COMP, EJ) of the citations used in comparison with the Spanish group (AT, AP, REF, EV). Moreover, the Introduction´s structure demonstrates that the Filipino writers put more emphasis on the contextualization of their study (M1) while the Spanish group highlights the presentation of their research (M3) that precedes the Introduction section.