We report on the experimental analysis of the charge transport through single-molecule junctions of the open and closed isomers of photoswitching molecules. Sulfur-free diarylethene molecules are developed and studied via electrical and optical measurements as well as density functional theory calculations. The single-molecule conductance and the current-voltage characteristics are measured in a mechanically controlled break-junction system at low temperatures. Comparing the results with the single-level transport model, we find an unexpected behavior of the current-dominating molecular orbital upon isomerization. We show that both the side chains and end groups of the molecules are crucial to understand the charge transport mechanism of photoswitching molecular junctions.