Provided herein are multi-probe systems and methods for amplifying and/or detecting multiple nucleic acid targets in a sample. The multi-probe systems comprise two or more probes having identical and/or different labels and are used together to target two or more related signature sequences in a genus, a species, or a gene. The probes comprise one or more probe:antiprobe systems selected from iDDS probes, iDDS-2Q probes, MacMan probes, Flip probes, Universal probes, Half-Universal probes, ZIPR probes, and G-Force probes. The probes are generally flanked by one set of primers, one primer, one primer-probe, or two primers. The methods utilize the multi-probe systems in real time PCR analysis for facilitating the assessment and/or diagnosis of nucleic acid sequences by providing confirmation of target detection and/or by providing greater signaling per test.