Brain signals are often analyzed in the spectral domain, where the power spectral density (PSD) and phase differences and consistency can reveal important information about the network. However, for proper interpretation, it is important to know whether these measures depend on stimulus/behavioral conditions or the reference scheme used to analyze data. We recorded local field potential (LFP) from an array of microelectrodes chronically implanted in area V1 of monkeys under different stimulus/behavioral conditions and computed PSD slopes, coherence, and phase difference between LFPs as a function of frequency and interelectrode distance while using four reference schemes: single wire, average, bipolar, and current source density. PSD slopes were dependent on reference scheme at low frequencies (below 200 Hz) but became invariant at higher frequencies. Average phase differences between sites also depended critically on referencing, switching from 0 degrees for single-wire to 180 degrees for average reference. Results were consistent across different stimulus/behavioral conditions. We were able to account for these results based on the coherence profile across sites and properties of the spectral estimator. Our results show that using different reference schemes can have drastic effects on phase differences and PSD slopes and therefore must be interpreted carefully to gain insights about network properties.