Microarrays are a limited method of sequencing a genome. They require DNA probes to be designed before the sample is assayed, and therefore require an understanding of the genome being looked at.
Due to their requirement for target probes to be bound to the microarray slide, there are a limited number of probes that can be used, conveying a limit to the size of the genome that can be used (if the whole genome is being used).
Non-specific binding (including wobble base-pairs) can also reduce the accuracy of microarrays, making it harder to be certain a given sequence is present in the DNA of interest.
Microarrays are not a good sequencing technology, but can be used successfully in transcriptomics and where there is a good understanding of the DNA being studied.