The rhyme scheme of “The Flea” is the same in each of its three stanzas: aabbccddd. So, for instance, in the first stanza we have “this / is,” “thee / be,” “said / maidenhead,” and “woo / two / do.”
In the opening rhyme of the second stanza, we have “spare / are,” which on the face of it doesn't sound like a rhyme until we remember the different pronunciations of certain words in Donne's time. In those days, “spare” did indeed rhyme with “are.”
The structure of the poem is somewhat unusual as nine-line stanzas are quite rare in English poetry. And the alternating use of meter in each stanza is doubly so.
In the first six lines of the stanza, we see an alternation between iambic tetrameter—a line of verse with four metrical feet, each one consisting of an unstressed syllable followed by a stressed one—and iambic pentameter, five metrical feet with each one consisting of an unstressed syllable followed by a stressed one.
Let's look at an example of this from the first stanza of “The Flea”:
Mark but this flea, and mark in this, [Iambic tetrameter]
How little that which thou deniest me is [Iambic pentameter].
The structure of the poem may seem rather unusual, but there's a reason for it. Donne wants to convey the somewhat unstable relationship between the speaker and his beloved.
The rhyme scheme may pull the lovers more closely together, but the irregular meter does the precise opposite. This constant toing and froing perfectly encapsulates the fact that, despite being lovers, the speaker and his lady are not quite on the same wavelength. If the rhyme scheme shows what the speaker would like this relationship to be, the ragged structure of the poem shows where it actually is.