Reasoning across descriptive levels is a fundamental component of scientific reasoning, particularly in chemistry. Repeatedly, students are seen to confuse features applicable to one level across multiple levels despite instruction. Although many instances of such "levels confusion" have been documented, little is known about the generation or reconciliation of levels confusion in the science classroom. The present study examines the nature of teacher-student discourse practices that generate, maintain, and reconcile levels confusion in chemistry. We present two case studies of whole class discussions of chemical and physical changes to illustrate how teachers and students enter the chemistry classroom biased to reason about chemistry phenomena from very different descriptive levels. Microanalysis of teacher-student discourse practices show how teachers implicitly refer to multiple descriptive levels during instruction and employ technical definitions and heuristics that tacitly appeal to multiple levels simultaneously. Our analysis suggests that levels confusion in chemistry arises from multiples sources that include the epistemological assumptions of chemistry, representational practices of the domain, and epistemological moves made by teachers in classroom discourse.