Researchers have reported persuasive evidence that students' perceptions of their classroom learning environment account for significant variance in cognitive and affective outcomes (e.g. intrinsic motivation, self-concept, liking for particular subjects and students' intention to drop out). The study reported in this paper investigated the relationship between students' perceptions of classroom learning environment and motivational achievement goal orientations towards biology and physics, as well as the influence of gender. Participants (N = 1538) were high school science students from the north-eastern region of Thailand. Our results suggest that motivational goals are linked to differences in students' perceptions of learning environment and levels of biology and physics classroom anxiety. We found that females adopted significantly higher levels of mastery and performance approach goals towards biology, while males adopted significantly higher levels of mastery and performance approach goals towards physics. Males adopted significantly higher levels of performance avoidance goals towards both biology and physics. Positive associations emerged between gender and the adoption of specific performance goals, perceived degree of competition in biology and physics classrooms, and levels of biology and physics classroom anxiety. These results suggest that motivational goal orientations and perceptions of learning environment are gender-dependent and domain-specific for the two science content areas.