The realisation to integrate science, ethics and morality is recognised with growing impetus in recent years (as noted with introducing the Australian Curriculum "Science as a Human Endeavour" strand), to develop sophisticated epistemologies of science, which includes an appreciation of the social context including ethical thinking. To fulfil the aim where pedagogy and curriculum enable students to integrate ideas about scientific issues and their own values, beliefs and ethics, educators need to understand how an individual naturally construes these issues. This paper is based on an investigation to address the need, in particular, how students construe genetic engineering issues as ethical issues and/or moral problems and how these values (faith/beliefs) influence their decision making regarding these issues, in a ten-week Year 10 biotechnology program in a faith-based school. Using an interpretative case study approach, a mixed method data collection and action research, analyses of instructional strategies, students' beliefs/values/attitudes and achievement outcomes were evaluated. The investigation is unique as it presents one of the few studies that incorporate faith values in the ethical frameworks, to explore the connection between cognitive learning, moral reasoning and moral development, and in the wider sense, between scientific literacy and ethical reasoning. It suggests that allegiance to belief systems and ideologies can sometimes override the influence of one's own sense of fairness in making decisions of moral rightness, and this has implications in mapping out curriculum for moral education and socio-scientific education.