Genotype refers to the genes that give a particular phenotype to an organism. For example, the flagellin gene codes for the protein flagellin which makes up the bacterial flagella.
In sexual reproducing organisms, a genotype is the two alleles that an individual has of a certain gene. An individual can either be homozygous, meaning they have two of the same alleles, or heterozygous, meaning they have two different alleles. These alleles are a mixture of the inherited alleles from the dam and sire of that offspring. In asexual reproducing organisms, the genotype is an exact copy of the "parent" cell, with no new introduction of alleles.