Methods and systems are provided for creating molecular barcodes or indicia for cellular constituents within single cells and for resolving such barcodes or indicia with super resolution technologies such as super resolution microscopy. By this approach, numerous molecular species that can be measured simultaneously in single cells. It has been demonstrated that multiple mRNA transcripts can be labeled with a spatially ordered sequence of fluorophores, and that barcode can be resolved. The methods and systems can be used for genome-wide transcriptional profiling in individual cells by super-resolution barcoding and suggest a general strategy to bring large-scale-omics approach into single cells.